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- PDB-9gzl: Apo FeFe Hydrogenase from Desulfovibrio desulfuricans labelled wi... -

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Basic information

Entry
Database: PDB / ID: 9gzl
TitleApo FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine
Components(Periplasmic [Fe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / Metalloprotein Iron-sulfur cluster Electron transfer
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
: / 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: 1.02 Å
AuthorsCarr, S.B. / Duan, Z. / Rodriguez-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 Multi-Centre 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 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)54,65515
Polymers53,3312
Non-polymers1,32413
Water10,431579
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint-197 kcal/mol
Surface area18050 Å2
Unit cell
Length a, b, c (Å)50.460, 88.005, 92.859
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: Protein 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 , 4 types, 592 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Li
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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 in 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: 0.77 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77 Å / Relative weight: 1
ReflectionResolution: 1.02→63.9 Å / Num. obs: 209983 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 11.53 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.027 / Net I/σ(I): 10.9
Reflection shellResolution: 1.02→1.04 Å / Redundancy: 7.9 % / Rmerge(I) obs: 2.7 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 10197 / CC1/2: 0.3 / Rpim(I) all: 0.99 / % possible all: 97.5

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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: 1.02→46.43 Å / SU ML: 0.1299 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.3173
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1533 10457 5.02 %
Rwork0.1392 197991 -
obs0.1399 208448 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.16 Å2
Refinement stepCycle: LAST / Resolution: 1.02→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3723 0 34 579 4336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863962
X-RAY DIFFRACTIONf_angle_d1.09845399
X-RAY DIFFRACTIONf_chiral_restr0.086576
X-RAY DIFFRACTIONf_plane_restr0.0114695
X-RAY DIFFRACTIONf_dihedral_angle_d6.0823546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.030.41832510.41935208X-RAY DIFFRACTION78.12
1.03-1.040.42313660.38976369X-RAY DIFFRACTION97.06
1.04-1.060.35683590.35846544X-RAY DIFFRACTION99.97
1.06-1.070.32883390.32626617X-RAY DIFFRACTION99.99
1.07-1.080.3023620.2936563X-RAY DIFFRACTION99.97
1.08-1.10.28673540.26516605X-RAY DIFFRACTION100
1.1-1.110.23643550.23856586X-RAY DIFFRACTION99.97
1.11-1.130.22413620.2376581X-RAY DIFFRACTION99.94
1.13-1.150.23623420.22436613X-RAY DIFFRACTION99.91
1.15-1.170.21823600.21676587X-RAY DIFFRACTION99.97
1.17-1.190.20713700.19446584X-RAY DIFFRACTION99.96
1.19-1.210.20453160.17926663X-RAY DIFFRACTION99.97
1.21-1.230.17933680.16866579X-RAY DIFFRACTION99.97
1.23-1.260.19273470.16456620X-RAY DIFFRACTION99.91
1.26-1.280.1863230.166638X-RAY DIFFRACTION99.97
1.28-1.310.17493510.14886596X-RAY DIFFRACTION99.96
1.31-1.350.15523020.14396692X-RAY DIFFRACTION99.93
1.35-1.380.16793560.13966612X-RAY DIFFRACTION99.96
1.38-1.420.15143850.13116624X-RAY DIFFRACTION99.99
1.42-1.470.15033570.12896641X-RAY DIFFRACTION99.99
1.47-1.520.13333660.11156652X-RAY DIFFRACTION99.99
1.52-1.580.12043380.10736647X-RAY DIFFRACTION99.96
1.58-1.660.12953950.10166629X-RAY DIFFRACTION100
1.66-1.740.11383530.10186666X-RAY DIFFRACTION99.99
1.74-1.850.12243170.10476749X-RAY DIFFRACTION99.99
1.85-20.11373570.10286698X-RAY DIFFRACTION100
2-2.20.11653130.10066770X-RAY DIFFRACTION100
2.2-2.510.12573460.11116780X-RAY DIFFRACTION100
2.51-3.170.14363400.13416834X-RAY DIFFRACTION100
3.17-46.430.14234070.13417044X-RAY DIFFRACTION100

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