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- PDB-8rxj: Nitratidesulfovibrio vulgaris [FeFe] hydrogenase C178A mutant in ... -

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Basic information

Entry
Database: PDB / ID: 8rxj
TitleNitratidesulfovibrio vulgaris [FeFe] hydrogenase C178A mutant in Hinact-like state derivatized with krypton
Components(Periplasmic [Fe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / [FeFe] hydrogenase / inhibitor / iron-sulfur cluster / gas channel / krypton
Function / homology
Function and homology information


ferredoxin hydrogenase / ferredoxin hydrogenase activity / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / 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-402 / CYANIDE ION / KRYPTON / IRON/SULFUR CLUSTER / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Periplasmic [Fe] hydrogenase large subunit / Periplasmic [Fe] hydrogenase small subunit
Similarity search - Component
Biological speciesNitratidesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.507 Å
AuthorsBikbaev, K. / Harand, T. / Scheuenstuhl, L. / Carpentier, P. / Span, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SP 1476/4-1 Germany
CitationJournal: To Be Published
Title: Krypton Derivatization of [FeFe] Hydrogenase from Desulfovibrio desulfuricans Reveals its Gas Channel
Authors: Bikbaev, K. / Harand, T. / Scheuenstuhl, L. / Carpentier, P. / Martini, M.A. / Birrell, J.A. / Span, I.
History
DepositionFeb 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2026Group: Source and taxonomy / Structure summary / Category: entity_src_gen / struct
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.title

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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)56,88618
Polymers54,4472
Non-polymers2,43816
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-117 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.376, 86.931, 88.889
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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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: 44365.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratidesulfovibrio vulgaris (bacteria)
Gene: hydA, DVU_1769 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): (delta)iscR / 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.) Nitratidesulfovibrio vulgaris (bacteria)
Gene: hydB, DVU_1770 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): (delta)iscR / References: UniProt: P07603, ferredoxin hydrogenase

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Non-polymers , 6 types, 236 molecules

#3: Chemical
ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Kr / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-402 / dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)


Mass: 354.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5Fe2N3O3S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H16O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 1 M Lithium chloride, 0.1 M Sodium acetate, 35 % Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.861 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Sep 29, 2023
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.861 Å / Relative weight: 1
ReflectionResolution: 1.507→43.503 Å / Num. obs: 60747 / % possible obs: 99.2 % / Redundancy: 10.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.057 / Rrim(I) all: 0.138 / Χ2: 0.99 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.25-43.478.30.05831.74350.9960.0280.0651.197.9
1.51-1.5311.41.8511.525140.6040.8172.0270.9684.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
PHASERphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.507→43.503 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.19 / WRfactor Rwork: 0.156 / SU B: 1.644 / SU ML: 0.058 / Average fsc free: 0.9695 / Average fsc work: 0.9763 / Cross valid method: NONE / ESU R: 0.075 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.186 3160 5.208 %
Rwork0.1583 57516 -
all0.16 --
obs-60676 99.178 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.261 Å2
Baniso -1Baniso -2Baniso -3
1-1.535 Å2-0 Å20 Å2
2---0.47 Å2-0 Å2
3----1.065 Å2
Refinement stepCycle: LAST / Resolution: 1.507→43.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 64 220 3996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123847
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163512
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.8395250
X-RAY DIFFRACTIONr_angle_other_deg0.6281.7438137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3525490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.281515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10210607
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.10710148
X-RAY DIFFRACTIONr_chiral_restr0.130.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024415
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02797
X-RAY DIFFRACTIONr_nbd_refined0.2450.2859
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.23249
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21904
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21885
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2152
X-RAY DIFFRACTIONr_metal_ion_refined0.0930.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3820.221
X-RAY DIFFRACTIONr_nbd_other0.2670.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.214
X-RAY DIFFRACTIONr_mcbond_it1.7132.0541944
X-RAY DIFFRACTIONr_mcbond_other1.7132.0541943
X-RAY DIFFRACTIONr_mcangle_it2.4173.6882430
X-RAY DIFFRACTIONr_mcangle_other2.4173.6882431
X-RAY DIFFRACTIONr_scbond_it2.5032.2421903
X-RAY DIFFRACTIONr_scbond_other2.5022.2431904
X-RAY DIFFRACTIONr_scangle_it3.6574.0232776
X-RAY DIFFRACTIONr_scangle_other3.6564.0242777
X-RAY DIFFRACTIONr_lrange_it4.59421.8454357
X-RAY DIFFRACTIONr_lrange_other4.59421.8474358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.507-1.5460.2921910.26938300.2744730.9320.93789.89490.265
1.546-1.5890.2642060.2441620.24143700.9490.95399.95420.234
1.589-1.6350.2352230.2239750.22141980.9550.961000.209
1.635-1.6850.232120.20738840.20840960.9580.9661000.192
1.685-1.740.2122340.18537630.18639970.9680.9741000.169
1.74-1.8010.1872260.16836180.1738500.9740.9899.84420.151
1.801-1.8690.1871720.1535540.15237260.9760.9841000.133
1.869-1.9450.1951660.14134570.14336230.9770.9871000.125
1.945-2.0310.1731530.13933070.14134600.9810.9871000.125
2.031-2.130.1851830.13831210.1433040.980.9881000.126
2.13-2.2450.1751980.13429610.13631600.9820.98999.96840.123
2.245-2.3810.1761620.14328300.14429920.9830.9881000.133
2.381-2.5450.1881390.15826840.15928240.9810.98699.96460.15
2.545-2.7480.181460.15524820.15626310.9810.98699.8860.151
2.748-3.0090.1931340.17222900.17324250.9750.98299.95880.173
3.009-3.3620.1841090.17121150.17222240.9790.9811000.177
3.362-3.8780.1781100.14718560.14919680.9830.98899.89840.161
3.878-4.740.147910.12615930.12716870.9880.99199.82220.144
4.74-6.6650.132580.13912860.13813450.990.98999.92570.159
6.665-43.5030.237470.1667480.1698060.8990.98298.63520.212

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