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- PDB-7m1n: Wild-type Hydrogenobacter thermophilus ferredoxin 1 -

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Basic information

Entry
Database: PDB / ID: 7m1n
TitleWild-type Hydrogenobacter thermophilus ferredoxin 1
ComponentsPutative ferredoxin
KeywordsELECTRON TRANSPORT
Function / homology4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / IRON/SULFUR CLUSTER / Putative ferredoxin
Function and homology information
Biological speciesHydrogenobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 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)16,6114
Polymers15,9082
Non-polymers7032
Water2,414134
1
A: Putative ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3062
Polymers7,9541
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3062
Polymers7,9541
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.)90.000, 90.000, 90.000
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-271-

HOH

21B-234-

HOH

31B-246-

HOH

41B-256-

HOH

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Components

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


Mass: 7953.935 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.: 134 / 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: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 79% 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 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.06→28 Å / Num. obs: 15621 / % possible obs: 98.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.0650310623 Å2 / CC1/2: 0.98 / Net I/σ(I): 2.2
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 2.1 % / Num. unique obs: 2921 / CC1/2: 0.76 / % possible all: 88.9

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Processing

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

1iqz


Resolution: 2.06→28 Å / SU ML: 0.192028364882 / Cross valid method: FREE R-VALUE / σ(F): 1.34748017906 / Phase error: 21.5958856637 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.212954664564 1557 9.97757129125 %
Rwork0.192554271328 14048 -
obs0.19465925904 15605 98.4045907428 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.1412151389 Å2
Refinement stepCycle: LAST / Resolution: 2.06→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 16 134 1234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01344124792671158
X-RAY DIFFRACTIONf_angle_d2.758456819661601
X-RAY DIFFRACTIONf_chiral_restr0.0355841431777175
X-RAY DIFFRACTIONf_plane_restr0.00353704188748213
X-RAY DIFFRACTIONf_dihedral_angle_d10.0694193413441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.1220.2825453142841280.2440430838691148X-RAY DIFFRACTION87.8183069511
2.122-2.19780.2416630051831400.2393980247291291X-RAY DIFFRACTION99.2371705964
2.1978-2.28580.2619998785161440.2253700896491280X-RAY DIFFRACTION99.4413407821
2.2858-2.38980.2132607045611470.2188293754221306X-RAY DIFFRACTION99.3844049248
2.3898-2.51570.2527816358141430.2156174713011269X-RAY DIFFRACTION99.7879858657
2.5157-2.67320.2418343905021410.2104301759291289X-RAY DIFFRACTION100
2.6732-2.87940.2207709953551470.204969305121299X-RAY DIFFRACTION100
2.8794-3.16880.2162923177431400.2072997042031289X-RAY DIFFRACTION99.5125348189
3.1688-3.62650.1821117905381490.1614986670511327X-RAY DIFFRACTION100
3.6265-4.56580.1771403604161370.1513958004481267X-RAY DIFFRACTION99.433427762
4.5658-280.188309526311410.1702525455711283X-RAY DIFFRACTION98.2068965517

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