BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 11-17-2010, 11:15 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Solution structure of the oxidized Fe7S8 ferredoxin from the thermophilic bacterium B

Solution structure of the oxidized Fe7S8 ferredoxin from the thermophilic bacterium Bacillus schlegelii by 1H NMR spectroscopy.

Related Articles Solution structure of the oxidized Fe7S8 ferredoxin from the thermophilic bacterium Bacillus schlegelii by 1H NMR spectroscopy.

Biochemistry. 1998 Jul 7;37(27):9812-26

Authors: Aono S, Bentrop D, Bertini I, Donaire A, Luchinat C, Niikura Y, Rosato A

The solution structure of the paramagnetic seven-iron ferredoxin from Bacillus schlegelii in its oxidized form has been determined by 1H NMR. The protein, which contains 77 amino acids, is thermostable. Seventy-two residues and 79% of all theoretically expected proton resonances have been assigned. The structure has been determined through torsion angle dynamics calculations with the program DYANA, using 966 meaningful NOEs (from a total of 1305), hydrogen bond constraints, and NMR derived dihedral angle constraints for the cluster ligating cysteines, and by using crystallographic information to build up the two clusters. Afterwards, restrained energy minimization and restrained molecular dynamics were applied to each conformer of the family. The final family of 20 structures has RMSD values from the mean structure of 0.68 A for the backbone atoms and of 1.16 A for all heavy atoms. The contributions to the thermal stability of the B. schlegelii ferredoxin are discussed by comparing the present structure to that of the less stable Azotobacter vinelandii ferredoxin I which is the only other available structure of a bacterial seven-iron ferredoxin. It is proposed that the hydrophobic interactions and the hydrogen bond network linking the N-terminus and the C-terminus together and a high number of salt bridges contribute to the stability.

PMID: 9657695 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Solution NMR structure of the cold-shock protein from the hyperthermophilic bacterium
Solution NMR structure of the cold-shock protein from the hyperthermophilic bacterium Thermotoga maritima. Related Articles Solution NMR structure of the cold-shock protein from the hyperthermophilic bacterium Thermotoga maritima. Eur J Biochem. 2001 May;268(9):2527-39 Authors: Kremer W, Schuler B, Harrieder S, Geyer M, Gronwald W, Welker C, Jaenicke R, Kalbitzer HR Cold-shock proteins (Csps) are a subgroup of the cold-induced proteins preferentially expressed in bacteria and other organisms on reduction of the growth temperature below the...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] 800 MHz 1H NMR solution structure refinement of oxidized cytochrome c7 from Desulfuro
800 MHz 1H NMR solution structure refinement of oxidized cytochrome c7 from Desulfuromonas acetoxidans. Related Articles 800 MHz 1H NMR solution structure refinement of oxidized cytochrome c7 from Desulfuromonas acetoxidans. Eur J Biochem. 1998 Sep 1;256(2):261-70 Authors: Assfalg M, Banci L, Bertini I, Bruschi M, Turano P The solution structure of Desulfuromonas acetoxidans cytochrome c7 has been refined by using 1H-NMR spectra recorded at 800 MHz and by using pseudocontact shifts in the final energy minimization procedure. The protein,...
nmrlearner Journal club 0 11-17-2010 11:15 PM
[NMR paper] 1H and 15N NMR resonance assignments and solution secondary structure of oxidized Des
1H and 15N NMR resonance assignments and solution secondary structure of oxidized Desulfovibrio desulfuricans flavodoxin. Related Articles 1H and 15N NMR resonance assignments and solution secondary structure of oxidized Desulfovibrio desulfuricans flavodoxin. J Biomol NMR. 1996 May;7(3):225-35 Authors: Pollock JR, Swenson RP, Stockman BJ Sequence-specific 1H and 15N resonance assignments have been made for 137 of the 146 nonprolyl residues in oxidized Desulfovibrio desulfuricans flavodoxin. Assignments were obtained by a concerted analysis...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] NMR characterization and solution structure determination of the oxidized cytochrome
NMR characterization and solution structure determination of the oxidized cytochrome c7 from Desulfuromonas acetoxidans. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-pnas_full_free.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles NMR characterization and solution structure determination of the oxidized cytochrome c7 from Desulfuromonas acetoxidans. Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14396-400 ...
nmrlearner Journal club 0 08-22-2010 02:20 PM
[NMR paper] An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-
An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin from Pseudomonas. Related Articles An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin from Pseudomonas. Biochemistry. 1994 May 31;33(21):6424-32 Authors: Pochapsky TC, Ye XM, Ratnaswamy G, Lyons TA A model for the solution structure of oxidized putidaredoxin (Pdx), a 106-residue globular protein containing a Fe2S2 cluster, has been determined using homonuclear NMR methods. Pdx is the first of the...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-
An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin from Pseudomonas. Related Articles An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin from Pseudomonas. Biochemistry. 1994 May 31;33(21):6424-32 Authors: Pochapsky TC, Ye XM, Ratnaswamy G, Lyons TA A model for the solution structure of oxidized putidaredoxin (Pdx), a 106-residue globular protein containing a Fe2S2 cluster, has been determined using homonuclear NMR methods. Pdx is the first of the...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] 1H NMR studies on the oxidized ferredoxin from Clostridium pasteurianum.
1H NMR studies on the oxidized ferredoxin from Clostridium pasteurianum. Related Articles 1H NMR studies on the oxidized ferredoxin from Clostridium pasteurianum. Biochem Int. 1992 Mar;26(4):577-85 Authors: Ganadu ML, Bonomi F, Pagani S, Boelens R The 8Fe-8S ferredoxin from Clostridium pasteurianum was investigated by 1D and 2D 1H NMR. Spectra of a well-structured, full native preparation of the oxidized protein in 1 M NaCl at pH 8.0 are presented. Assignments of non-isotropically shifted resonances in the diamagnetic region of the spectrum,...
nmrlearner Journal club 0 08-21-2010 11:41 PM
[NMR paper] Solution structure of the B form of oxidized rat microsomal cytochrome b5 and backbon
Solution structure of the B form of oxidized rat microsomal cytochrome b5 and backbone dynamics via 15N rotating-frame NMR-relaxation measurements. Biological implications. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Solution structure of the B form of oxidized rat microsomal cytochrome b5 and backbone dynamics via 15N rotating-frame NMR-relaxation measurements. Biological implications. Eur J Biochem. 1999 Mar;260(2):347-54 Authors: ...
nmrlearner Journal club 0 08-21-2010 04:03 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 06:25 PM.


Map