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- PDB-8rti: Nitratidesulfovibrio vulgaris [FeFe] hydrogenase in the apo form ... -

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Basic information

Entry
Database: PDB / ID: 8rti
TitleNitratidesulfovibrio vulgaris [FeFe] hydrogenase in the apo form derivatized with krypton
Components(Periplasmic [Fe] hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / [FeFe] hydrogenase / apo hydrogenase / 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
KRYPTON / TRIETHYLENE GLYCOL / IRON/SULFUR CLUSTER / Periplasmic [Fe] hydrogenase large subunit / Periplasmic [Fe] hydrogenase small subunit
Similarity search - Component
Biological speciesNitratidesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsBikbaev, K. / Carpentier, P. / Harand, T. / Scheuenstuhl, L. / 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
DepositionJan 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 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)55,8528
Polymers54,4802
Non-polymers1,3736
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-103 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.677, 88.048, 89.784
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 , 4 types, 297 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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 31.75 %
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: 1.5→44.932 Å / Num. obs: 63544 / % possible obs: 99.8 % / Redundancy: 9.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.073 / Rrim(I) all: 0.17 / Χ2: 0.94 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.22-44.897.60.0722.64670.9970.0340.0780.9699.7
1.5-1.5310.21.9281.229920.5350.9182.1390.9296.3

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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: 1.502→44.932 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.173 / SU B: 1.648 / SU ML: 0.058 / Average fsc free: 0.9681 / Average fsc work: 0.975 / Cross valid method: NONE / ESU R: 0.078 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1939 3285 5.176 %
Rwork0.1695 60180 -
all0.171 --
obs-63465 99.742 %
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: 19.113 Å2
Baniso -1Baniso -2Baniso -3
1-1.008 Å2-0 Å20 Å2
2---1.05 Å2-0 Å2
3---0.041 Å2
Refinement stepCycle: LAST / Resolution: 1.502→44.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 36 291 4034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123835
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163522
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.835230
X-RAY DIFFRACTIONr_angle_other_deg0.6131.748151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4545493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.671515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84310609
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.27910148
X-RAY DIFFRACTIONr_chiral_restr0.1150.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024428
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02800
X-RAY DIFFRACTIONr_nbd_refined0.2270.2800
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.23220
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21890
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21869
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2214
X-RAY DIFFRACTIONr_metal_ion_refined0.130.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2520.212
X-RAY DIFFRACTIONr_nbd_other0.2010.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.223
X-RAY DIFFRACTIONr_mcbond_it1.611.7941946
X-RAY DIFFRACTIONr_mcbond_other1.6091.7941946
X-RAY DIFFRACTIONr_mcangle_it2.253.2262436
X-RAY DIFFRACTIONr_mcangle_other2.253.2262437
X-RAY DIFFRACTIONr_scbond_it2.542.0041889
X-RAY DIFFRACTIONr_scbond_other2.542.0061890
X-RAY DIFFRACTIONr_scangle_it3.6773.5632754
X-RAY DIFFRACTIONr_scangle_other3.6763.5642755
X-RAY DIFFRACTIONr_lrange_it4.92619.3444341
X-RAY DIFFRACTIONr_lrange_other4.86718.5514289
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
1.502-1.540.3312120.32143090.32246370.9320.93497.49840.323
1.54-1.5830.3092470.28942720.2945190.9460.9461000.288
1.583-1.6280.2741930.24642200.24744130.9510.9611000.242
1.628-1.6790.262380.2240250.22342660.9560.96899.92970.213
1.679-1.7330.2332320.19539070.19741420.9670.97599.92760.184
1.733-1.7940.2292030.17938410.18240450.9620.97999.97530.168
1.794-1.8620.1981900.1636740.16238640.9770.9841000.15
1.862-1.9380.2042350.15735010.1637380.9730.98599.94650.149
1.938-2.0240.1791680.16134220.16235900.9830.9851000.152
2.024-2.1220.1931590.16532910.16634510.9770.98599.9710.159
2.122-2.2370.1971730.15431080.15632810.9790.9871000.148
2.237-2.3720.1861670.14929650.15131370.9790.98799.84060.145
2.372-2.5350.1851420.15327620.15429120.980.98599.72530.151
2.535-2.7380.1611300.14426140.14527450.9840.98799.96360.143
2.738-2.9980.1781240.15824130.15925370.980.9841000.16
2.998-3.350.2231260.17121680.17422960.9690.98299.91290.178
3.35-3.8650.1661120.15419360.15520510.9850.98699.85370.167
3.865-4.7250.1451000.13816550.13817580.9870.9999.82940.155
4.725-6.6450.166700.17113230.1713940.9890.98899.92830.191
6.645-44.9320.205640.2017740.2018390.970.96999.88080.348

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