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- PDB-8rxi: Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in Hinact state ... -

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Basic information

Entry
Database: PDB / ID: 8rxi
TitleNitratidesulfovibrio vulgaris [FeFe] hydrogenase in Hinact 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 / 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
KRYPTON / Chem-LFH / 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: 1.477 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)56,2539
Polymers54,4802
Non-polymers1,7747
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-109 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.6, 87.967, 89.71
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: 44397.098 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 , 5 types, 359 molecules

#3: Chemical ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Kr / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#6: Chemical ChemComp-LFH / dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+) sulphide


Mass: 387.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5Fe2N3O3S3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 1 M Lithium chloride, 0.1 M Sodium acetate, 40 % 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: 1.477→44.895 Å / Num. obs: 66193 / % possible obs: 99.3 % / Redundancy: 8.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.057 / Rrim(I) all: 0.123 / Χ2: 1.01 / Net I/σ(I): 10.9
Reflection shellResolution: 1.48→1.5 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.327 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2817 / CC1/2: 0.658 / Rpim(I) all: 0.7 / Rrim(I) all: 1.505 / Χ2: 0.9 / % possible all: 86.1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0425refinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.477→44.895 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.343 / SU ML: 0.049 / Cross valid method: NONE / ESU R: 0.069 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1811 3301 4.993 %
Rwork0.1542 62817 -
all0.156 --
obs-66118 99.279 %
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: 17.501 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å2-0 Å2
2---0.911 Å2-0 Å2
3---0.301 Å2
Refinement stepCycle: LAST / Resolution: 1.477→44.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 54 352 4113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123866
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163542
X-RAY DIFFRACTIONr_angle_refined_deg2.1061.8395281
X-RAY DIFFRACTIONr_angle_other_deg0.6611.7438203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4455499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.005515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13910614
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.26310149
X-RAY DIFFRACTIONr_chiral_restr0.1370.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024455
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02801
X-RAY DIFFRACTIONr_nbd_refined0.2320.2835
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.23348
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21915
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21873
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2255
X-RAY DIFFRACTIONr_metal_ion_refined0.1140.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2960.216
X-RAY DIFFRACTIONr_nbd_other0.2320.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0250.21
X-RAY DIFFRACTIONr_mcbond_it1.5051.6381952
X-RAY DIFFRACTIONr_mcbond_other1.5051.6381952
X-RAY DIFFRACTIONr_mcangle_it2.1132.9432445
X-RAY DIFFRACTIONr_mcangle_other2.1132.9432446
X-RAY DIFFRACTIONr_scbond_it2.3091.8231914
X-RAY DIFFRACTIONr_scbond_other2.3081.8241915
X-RAY DIFFRACTIONr_scangle_it3.2943.2522794
X-RAY DIFFRACTIONr_scangle_other3.2933.2532795
X-RAY DIFFRACTIONr_lrange_it4.34718.7494472
X-RAY DIFFRACTIONr_lrange_other4.25717.714385
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
1.477-1.5150.3052300.28442100.28648710.9410.94991.15170.28
1.515-1.5570.2772300.24645090.24847420.9490.95999.93670.241
1.557-1.6020.2542090.20944130.2146250.960.97199.93510.199
1.602-1.6510.2042290.18742420.18844740.9730.97799.93290.175
1.651-1.7050.1842250.16440900.16543180.9790.98399.93050.149
1.705-1.7650.2082000.15840270.1642270.9730.9841000.144
1.765-1.8320.1771870.14738740.14940630.9810.98699.95080.133
1.832-1.9060.1691770.14337470.14439250.9810.98899.97450.13
1.906-1.9910.1761950.13835580.1437540.9810.98899.97340.126
1.991-2.0880.1631970.14433800.14535790.9850.98899.94410.134
2.088-2.2010.1761710.14232630.14434350.9820.98899.97090.133
2.201-2.3340.1681450.13731130.13832600.9820.98999.93870.129
2.334-2.4940.1661700.13629020.13830720.9820.9891000.131
2.494-2.6930.1731500.13727070.13928570.9830.9881000.136
2.693-2.950.1841500.14525140.14726640.980.9871000.147
2.95-3.2960.1951190.16122990.16224180.9760.9841000.165
3.296-3.8020.158890.15120480.15121380.9840.98799.95320.162
3.802-4.6490.1251060.12717250.12718340.990.99199.83640.144
4.649-6.5390.2780.15813630.1614420.9790.98999.93060.179
6.539-44.8950.227440.1848330.1868820.970.97899.43310.225

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