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- PDB-1e10: [2Fe-2S]-Ferredoxin from Halobacterium salinarum -

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Basic information

Entry
Database: PDB / ID: 10000000000
Title[2Fe-2S]-Ferredoxin from Halobacterium salinarum
ComponentsFERREDOXIN
KeywordsIRON-SULFUR PROTEIN / FERREDOXIN / HALOBACTERIUM SALINARUM / HALOPHILIC
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / FE2/S2 (INORGANIC) CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesHALOBACTERIUM HALOBIUM (Halophile)
MethodSOLUTION NMR / simulated annealing
AuthorsMarg, B.-L. / Schweimer, K. / Oesterhelt, D. / Roesch, P. / Sticht, H.
Citation
Journal: Biochemistry / Year: 2005
Title: A Two-Alpha-Helix Extra Domain Mediates the Halophilic Character of a Plant-Type Ferredoxin from Halophilic Archaea.
Authors: Marg, B. / Schweimer, K. / Sticht, H. / Oesterhelt, D.
#1: Journal: J.Biomol.NMR / Year: 2000
Title: Sequence-Specific 1H, 13C and 15N Resonance Assignments and Secondary Structure of [2Fe-2S] Ferredoxin from Halobacterium Salinarum
Authors: Schweimer, K. / Marg, B.-L. / Oesterhelt, D. / Roesch, P. / Sticht, H.
History
DepositionApr 12, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5153
Polymers14,2961
Non-polymers2202
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60LEAST RESTRAINT VIOLATION, LOWEST ENERGY
Representative

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Components

#1: Protein FERREDOXIN /


Mass: 14295.544 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOBACTERIUM HALOBIUM (Halophile) / References: UniProt: P00216
#2: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-1H NOESY
1211H-1H TOCSY
1311H-15N HSQC
1411H-13C CT-HSQC
15115N-EDITED NOESY(3D)
16113C-EDITED NO HNCO
171HNCA
181HN(CA)CB
191CBCA(CO)NH HBHA(CO)NH
1101HNHA
1111(H)CCH-COSY
1121(H)CCH-
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HETERONUCLEAR MULTIDIMENSIONAL NMR USING 15N- AND 13C,15N LABELED FERREDOXIN SAMPLES

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionsIonic strength: 500 mM / pH: 6.4 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
NMRVIEWstructure solution
NDEEstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. FOR RESIDUES 60-71, 87, AND 100-104 NO NMR DISTANCE RESTRAINTS WERE OBTAINED BECAUSE OF THE PROXIMITY TO THE PARAMAGNETIC IRON- ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. FOR RESIDUES 60-71, 87, AND 100-104 NO NMR DISTANCE RESTRAINTS WERE OBTAINED BECAUSE OF THE PROXIMITY TO THE PARAMAGNETIC IRON-SULFUR CLUSTER. THE CORRESPONDING RESIDUES WERE NOT RESTRAINED DURING THE STRUCTURE CALCULATION AND ARE THEREFORE ILL-DEFINED.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION, LOWEST ENERGY
Conformers calculated total number: 60 / Conformers submitted total number: 20

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