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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 / homology
Function and homology information


2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Thioredoxin-like [2Fe-2S] ferredoxin / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin, 2Fe-2S
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
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.
History
DepositionMay 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Polymers24,4122
Non-polymers5364
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-50 kcal/mol
Surface area10650 Å2
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
Polymers48,8254
Non-polymers1,0728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area5730 Å2
ΔGint-111 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
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-MP41212
Components on special symmetry positions
IDModelComponents
11A-2024-

HOH

DetailsThe biological assembly is a homodimer

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Components

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


Mass: 12206.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / 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 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 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
IDConc.Common 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 temperature (K)Crystal-ID
1901
2901
3901
4901
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL9-211.5001
SYNCHROTRONSSRL BL9-221.734
SYNCHROTRONSSRL BL9-231.7415
SYNCHROTRONSSRL BL9-241.7968
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 26, 1999
ADSC QUANTUM 42CCDJun 26, 1999
ADSC QUANTUM 43CCDJun 26, 1999
ADSC QUANTUM 44CCDJun 26, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.50011
21.7341
31.74151
41.79681
ReflectionResolution: 2.3→50 Å / Num. all: 11218 / Num. obs: 11218 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 24.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.277 / Num. unique all: 550 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 74834
Reflection shell
*PLUS
% possible obs: 99.8 % / Mean I/σ(I) obs: 5.3

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
Blu-Icedata collection
SCALEPACKdata scaling
RefinementResolution: 2.3→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: 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 ...Details: 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1506 -Approximately 7.5% of the data were randomly selected for the R-free test set.
Rwork0.225 ---
all0.228 20358 --
obs0.228 20358 99.5 %-
Refinement stepCycle: LAST / Resolution: 2.3→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 20 70 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
Refinement
*PLUS
% reflection Rfree: 7.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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