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- PDB-1f37: STRUCTURE OF A THIOREDOXIN-LIKE [2FE-2S] FERREDOXIN FROM AQUIFEX ... -

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Basic information

Entry
Database: PDB / ID: 1f37
TitleSTRUCTURE OF A THIOREDOXIN-LIKE [2FE-2S] FERREDOXIN FROM AQUIFEX AEOLICUS
ComponentsFERREDOXIN [2FE-2S]
KeywordsELECTRON TRANSPORT / ferredoxin / [2Fe-2S] cluster / thioredoxin fold
Function / homologyThioredoxin-like superfamily / Thioredoxin-like [2Fe-2S] ferredoxin / 2 iron, 2 sulfur cluster binding / oxidation-reduction process / metal ion binding / Ferredoxin, 2Fe-2S
Function and homology information
Specimen sourceAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2.3 Å resolution
AuthorsYeh, A.P. / Chatelet, C. / Soltis, S.M. / Kuhn, P. / Meyer, J. / Rees, D.C.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Structure of a thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus.
Authors: Yeh, A.P. / Chatelet, C. / Soltis, S.M. / Kuhn, P. / Meyer, J. / Rees, D.C.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 1999
Title: A [2Fe-2S] protein from the hyperthermophilic bacterium Aquifex aeolicus
Authors: Chatelet, C. / Gaillard, J. / Petillot, Y. / Louwagie, M. / Meyer, J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 31, 2000 / Release: Jul 26, 2000
RevisionDateData content typeGroupProviderType
1.0Jul 26, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERREDOXIN [2FE-2S]
B: FERREDOXIN [2FE-2S]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9486
Polyers24,4122
Non-polymers5364
Water1,26170
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)2310
ΔGint (kcal/M)-50
Surface area (Å2)10650
MethodPISA
2
A: FERREDOXIN [2FE-2S]
B: FERREDOXIN [2FE-2S]
hetero molecules

A: FERREDOXIN [2FE-2S]
B: FERREDOXIN [2FE-2S]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,89612
Polyers48,8254
Non-polymers1,0728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area (Å2)5730
ΔGint (kcal/M)-111
Surface area (Å2)20200
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)68.079, 68.079, 102.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP 41 21 2
DetailsThe biological assembly is a homodimer

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Components

#1: Protein/peptide FERREDOXIN [2FE-2S]


Mass: 12206.156 Da / Num. of mol.: 2 / Source: (gene. exp.) Aquifex aeolicus (bacteria) / Genus: Aquifex / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: O66511
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Formula: C3H8O3 / Glycerol
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 / Density percent sol: 49.4 %
Crystal growTemp: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: ammonium sulfate, p-dioxane, 2-(N-morpholino)-ethane sulfonic acid, pH 6.5, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and reservoir solutions
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
111 mg/mlprotein1drop
210 mMTris-HCl1drop
30.2 M1dropNaCl
41.6 Mammonium sulfate1reservoir
54-5 %(v/v)p-dioxane1reservoir
6100 mMMES1reservoir

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Data collection

Diffraction
IDMean temperatureCrystal ID
1901
2901
3901
4901
Source
SourceSiteBeamlineIdWavelength
SYNCHROTRONSSRL BL9-211.5001
SYNCHROTRONSSRL BL9-221.7340
SYNCHROTRONSSRL BL9-231.7415
SYNCHROTRONSSRL BL9-241.7968
Detector
TypeIdDetectorCollection date
ADSC QUANTUM 41CCD1999-06-26
ADSC QUANTUM 42CCD1999-06-26
ADSC QUANTUM 43CCD1999-06-26
ADSC QUANTUM 44CCD1999-06-26
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
11.50011.0
21.73401.0
31.74151.0
41.79681.0
ReflectionB iso Wilson estimate: 52.3 Å2 / D resolution high: 2.3 Å / D resolution low: 5 Å / Number all: 11218 / Number obs: 11218 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.055 / NetI over sigmaI: 24.8 / Redundancy: 6.7 % / Percent possible obs: 99.3
Reflection shellRmerge I obs: 0.277 / Highest resolution: 2.3 Å / Lowest resolution: 2.34 Å / Number unique all: 550 / Redundancy: 6.7 % / Percent possible all: 99.8
Reflection
*PLUS
Number measured all: 74834
Reflection shell
*PLUS
Percent possible obs: 99.8 / MeanI over sigI obs: 5.3

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
Blu-Icedata collection
SCALEPACKdata scaling
RefineDetails: The data that was used in the refinement was collected at a wavelength of 1.5001 Angstroms. Due to the iron anomalous signal resulting from collecting at this wavelength, the structure was refined against the separate Friedel mates. The reported number of reflections used in the refinement counts each mate of a Friedel pair as a separate reflection.
R Free selection details: Approximately 7.5% of the data were randomly selected for the R-free test set.
Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.27 / R factor R work: 0.225 / R factor all: 0.228 / R factor obs: 0.228 / Highest resolution: 2.3 Å / Lowest resolution: 5 Å / Number reflection R free: 1506 / Number reflection all: 20358 / Number reflection obs: 20358 / Percent reflection obs: 99.5
Refine hist #LASTHighest resolution: 2.3 Å / Lowest resolution: 5 Å
Number of atoms included #LASTProtein: 1692 / Nucleic acid: 0 / Ligand: 20 / Solvent: 70 / Total: 1782
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.53
Software
*PLUS
Name: 'CNS' / Classification: refinement
Least-squares process
*PLUS
Percent reflection R free: 7.5

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