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- PDB-9gz4: FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with c... -

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Basic information

Entry
Database: PDB / ID: 9gz4
TitleFeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - reduced state
Components(Periplasmic [Fe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / Metalloprotein Iron-sulfur cluster hydrogenase
Function / homology
Function and homology information


ferredoxin hydrogenase / ferredoxin hydrogenase activity / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / iron ion binding
Similarity search - Function
Iron hydrogenase, small subunit HydB-type / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase ...Iron hydrogenase, small subunit HydB-type / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Chem-4WW / : / IRON/SULFUR CLUSTER / Periplasmic [Fe] hydrogenase large subunit / Periplasmic [Fe] hydrogenase small subunit
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsCarr, S.B. / Duan, Z. / Rodroguez-Macia, P. / Vincent, K.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R018413/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X002624/1 United Kingdom
CitationJournal: Chembiochem / Year: 2025
Title: Cyanophenylalanine as an Infrared Probe for Iron-Sulfur Cluster Redox State in Multicenter Metalloenzymes.
Authors: Duan, Z. / Wei, J. / Carr, S.B. / Ramirez, M. / Evans, R.M. / Ash, P.A. / Rodriguez-Macia, P. / Sachdeva, A. / Vincent, K.A.
History
DepositionOct 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 30, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic [Fe] hydrogenase large subunit
B: Periplasmic [Fe] hydrogenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,85310
Polymers53,3312
Non-polymers1,5228
Water9,476526
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-142 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.718, 87.713, 89.885
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Periplasmic [Fe] hydrogenase ... , 2 types, 2 molecules AB

#1: Protein Periplasmic [Fe] hydrogenase large subunit / Fe hydrogenlyase


Mass: 43248.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Enzyme engineered to contain cyanophenylalanine (4CF) at position 27
Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Gene: hydA, DVU_1769 / Production host: Escherichia coli (E. coli) / References: UniProt: P07598, ferredoxin hydrogenase
#2: Protein Periplasmic [Fe] hydrogenase small subunit / Fe hydrogenlyase small chain


Mass: 10082.425 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Gene: hydB, DVU_1770 / Production host: Escherichia coli (E. coli) / References: UniProt: P07603, ferredoxin hydrogenase

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Non-polymers , 5 types, 534 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-4WW / bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) / propane-dithiolato-bridged [2Fe2S] cluster


Mass: 353.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6Fe2N2O3S2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 1.78 Å3/Da / Density % sol: 31 % / Description: Brown plates
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.9 M LiSO4 100 mM Na Acetate 24-30% Peg 6000 / Temp details: Ambient temperature of N2 filled glovebox

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.81 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 0.96→62.8 Å / Num. obs: 239126 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 8.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.032 / Net I/σ(I): 10.8
Reflection shellResolution: 0.96→0.98 Å / Redundancy: 10.3 % / Rmerge(I) obs: 2.2 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 11725 / CC1/2: 0.47 / Rpim(I) all: 0.74 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.96→44.94 Å / SU ML: 0.0994 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.7457
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1522 12122 5.08 %
Rwork0.1436 226687 -
obs0.1441 238809 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.6 Å2
Refinement stepCycle: LAST / Resolution: 0.96→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 0 45 526 4286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813932
X-RAY DIFFRACTIONf_angle_d1.17345363
X-RAY DIFFRACTIONf_chiral_restr0.0899572
X-RAY DIFFRACTIONf_plane_restr0.0121681
X-RAY DIFFRACTIONf_dihedral_angle_d6.1698536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.96-0.970.31753900.31787488X-RAY DIFFRACTION99.8
0.97-0.980.28923990.30527417X-RAY DIFFRACTION99.83
0.98-0.990.29324090.28277511X-RAY DIFFRACTION99.85
0.99-1.010.28053820.27387512X-RAY DIFFRACTION99.92
1.01-1.020.25744130.25117476X-RAY DIFFRACTION99.81
1.02-1.030.25414270.23827444X-RAY DIFFRACTION99.85
1.03-1.050.23274290.22597462X-RAY DIFFRACTION99.73
1.05-1.060.22814040.21167470X-RAY DIFFRACTION99.87
1.06-1.080.21983990.19657562X-RAY DIFFRACTION99.89
1.08-1.10.21144030.18757457X-RAY DIFFRACTION99.89
1.1-1.120.19583610.18397528X-RAY DIFFRACTION99.84
1.12-1.140.18224090.17697511X-RAY DIFFRACTION99.87
1.14-1.160.17334130.17027504X-RAY DIFFRACTION99.9
1.16-1.180.18684080.1587540X-RAY DIFFRACTION99.91
1.18-1.210.17354160.14997453X-RAY DIFFRACTION99.87
1.21-1.240.14593910.14837548X-RAY DIFFRACTION99.92
1.24-1.270.14894310.14457505X-RAY DIFFRACTION99.97
1.27-1.30.1554190.14117517X-RAY DIFFRACTION99.91
1.3-1.340.15653980.13697558X-RAY DIFFRACTION99.99
1.34-1.380.15953460.13867610X-RAY DIFFRACTION99.95
1.38-1.430.16313900.13127559X-RAY DIFFRACTION99.97
1.43-1.490.12863930.12527575X-RAY DIFFRACTION99.99
1.49-1.560.13253870.11947603X-RAY DIFFRACTION99.99
1.56-1.640.12114270.11017543X-RAY DIFFRACTION99.99
1.64-1.740.11443650.11117669X-RAY DIFFRACTION99.99
1.74-1.880.1154190.11187591X-RAY DIFFRACTION100
1.88-2.070.12194500.11347617X-RAY DIFFRACTION100
2.07-2.370.13014540.11547651X-RAY DIFFRACTION100
2.37-2.980.14343880.13467762X-RAY DIFFRACTION100
2.98-44.940.13714020.13978044X-RAY DIFFRACTION99.94

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