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- PDB-7m1o: Hydrogenobacter thermophilus ferredoxin 1 S64A variant -

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Basic information

Entry
Database: PDB / ID: 7m1o
TitleHydrogenobacter thermophilus ferredoxin 1 S64A variant
ComponentsPutative ferredoxin
KeywordsELECTRON TRANSPORT
Function / homology: / 4Fe-4S single cluster domain of Ferredoxin I / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4 iron, 4 sulfur cluster binding / metal ion binding / IRON/SULFUR CLUSTER / Putative ferredoxin
Function and homology information
Biological speciesHydrogenobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98388706704 Å
AuthorsSteindel, P.S. / Li, B. / Elliott, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)BES DE-SC0012598 United States
CitationJournal: Acs Catalysis / Year: 2021
Title: Maximizing (Electro)catalytic CO2 Reduction with a Ferredoxin-Based Reduction Potential Gradient
Authors: Li, B. / Steindel, P. / Haddad, N. / Elliott, S.J.
History
DepositionMar 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ferredoxin
B: Putative ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5794
Polymers15,8762
Non-polymers7032
Water1,76598
1
A: Putative ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2902
Polymers7,9381
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2902
Polymers7,9381
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.635, 69.103, 95.788
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

21A-256-

HOH

31B-223-

HOH

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Components

#1: Protein Putative ferredoxin / [4Fe-4S] ferredoxin 1


Mass: 7937.935 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrogenobacter thermophilus (bacteria)
Gene: fdx1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q75VV9
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 80% saturated ammonium sulfate, 0.1 M MES (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.98→56.23 Å / Num. obs: 17128 / % possible obs: 97.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 20.1385556239 Å2 / CC1/2: 0.991 / Net I/σ(I): 6
Reflection shellResolution: 1.98→2.06 Å / Num. unique obs: 1338 / CC1/2: 0.652

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IQZ

1iqz


Resolution: 1.98388706704→36.6235981261 Å / SU ML: 0.173665000433 / Cross valid method: FREE R-VALUE / σ(F): 1.33689107397 / Phase error: 22.0758782231
RfactorNum. reflection% reflection
Rfree0.218940886283 1707 9.97370727432 %
Rwork0.186116565067 15408 -
obs0.189498381145 17115 97.1559945504 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.9142152628 Å2
Refinement stepCycle: LAST / Resolution: 1.98388706704→36.6235981261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 16 98 1196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004772479846321134
X-RAY DIFFRACTIONf_angle_d1.124677461441586
X-RAY DIFFRACTIONf_chiral_restr0.050136334029172
X-RAY DIFFRACTIONf_plane_restr0.00353296620042204
X-RAY DIFFRACTIONf_dihedral_angle_d25.7744117824440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9839-2.04230.2761128563281090.269218238314940X-RAY DIFFRACTION71.5552523874
2.0423-2.10820.2992162920671420.2519257521061272X-RAY DIFFRACTION96.7168262654
2.1082-2.18350.2849287676291430.2275791496191327X-RAY DIFFRACTION99.593495935
2.1835-2.27090.2160366377641450.2092798999341310X-RAY DIFFRACTION99.8627316404
2.2709-2.37430.2152104477941480.1979005643411306X-RAY DIFFRACTION99.7940974605
2.3743-2.49940.2396901827871510.207310553551332X-RAY DIFFRACTION99.8653198653
2.4994-2.6560.252647608441430.203834596781328X-RAY DIFFRACTION100
2.656-2.8610.2485112542651480.2096925522781308X-RAY DIFFRACTION100
2.861-3.14870.2297354143711440.200323738321320X-RAY DIFFRACTION100
3.1487-3.6040.2083101106971480.1701153885371329X-RAY DIFFRACTION99.9323410014
3.604-4.53930.1632606435941430.1473719894161314X-RAY DIFFRACTION99.7945205479
4.5393-36.62359812610.1858674923531430.1426627289991322X-RAY DIFFRACTION98.8529014845

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