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- PDB-9gbu: Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both ... -

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Basic information

Entry
Database: PDB / ID: 9gbu
TitleDesulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from a group A1 type [FeFe]-hydrogenase of Solobacterium moorei
ComponentsPeriplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit
KeywordsOXIDOREDUCTASE / [FeFe] hydrogenase / iron-sulfur cluster / metalloenzyme / hydrogen production / fusion protein
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-402 / 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: 1.785 Å
AuthorsBikbaev, K. / Jaenecke, J. / Winkler, M. / Span, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SP 1476/4-1 Germany
CitationJournal: To Be Published
Title: Enhancing maturation of [FeFe]-hydrogenase by interlinking the large and small subunits
Authors: Bikbaev, K. / Jaenecke, J. / Winkler, M. / Span, I.
History
DepositionJul 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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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,Periplasmic [Fe] hydrogenase small subunit
B: Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,65916
Polymers108,1302
Non-polymers3,52914
Water3,981221
1
A: Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9489
Polymers54,0651
Non-polymers1,8838
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7117
Polymers54,0651
Non-polymers1,6466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.024, 98.814, 112.208
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 54064.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Gene: hydA, DVU_1769, hydB, DVU_1770 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): (delta)iscR
References: UniProt: P07598, UniProt: P07603, ferredoxin hydrogenase
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-402 / dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)


Mass: 354.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5Fe2N3O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 50% MPD, 0.1 HEPES pH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 25, 2024
RadiationMonochromator: Si-111 and Si-113 reflection / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.78→48.836 Å / Num. obs: 98395 / % possible obs: 99.6 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.041 / Rrim(I) all: 0.11 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
9.78-48.7911.30.0396970.9990.0160.0420.82
1.78-1.8213.62.14147680.5690.8642.3121.01

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
BUCCANEERmodel building
Cootmodel building
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.785→48.836 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 0.003 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.105 / ESU R Free: 0.127
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2416 4729 4.81 %
Rwork0.201 93588 -
all0.203 --
obs-98317 99.546 %
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: 41.898 Å2
Baniso -1Baniso -2Baniso -3
1--1.439 Å2-0 Å20 Å2
2--2.108 Å2-0 Å2
3----0.669 Å2
Refinement stepCycle: LAST / Resolution: 1.785→48.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7375 0 130 221 7726
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
1.785-1.8310.3283340.30268240.30372450.9170.92698.79920.3
1.831-1.8810.2873320.27166510.27169870.9320.94399.94270.263
1.881-1.9360.2973330.2565500.25268870.9350.95599.94190.239
1.936-1.9950.273270.24463000.24666350.9470.95899.87940.231
1.995-2.060.2623180.23261140.23464690.9540.96399.4280.215
2.06-2.1320.2693260.22158360.22462340.9520.96798.8450.204
2.132-2.2130.2633240.21256670.21560360.9560.9799.25450.193
2.213-2.3030.2422670.255340.20258110.9620.97499.82790.181
2.303-2.4050.2352650.18853190.1955970.9660.97899.76770.168
2.405-2.5220.2462360.19350980.19553450.9620.97699.79420.175
2.522-2.6580.2222490.19248240.19350870.9670.97799.72480.175
2.658-2.8190.2412140.19846220.248540.9670.97799.62920.184
2.819-3.0130.2552210.20643010.20945290.9610.97499.84540.195
3.013-3.2530.2641830.2140600.21242430.9540.971000.203
3.253-3.5620.2422000.20337400.20539400.9590.9721000.203
3.562-3.980.2321720.19932880.235590.9610.97597.21830.206
3.98-4.5910.2081480.17530150.17731740.9680.9899.65340.187
4.591-5.610.2281080.18425900.18626980.9690.9781000.199
5.61-7.8820.2411090.19620390.19921480.9560.9761000.215
7.882-48.8360.195630.16512160.16712810.9770.98199.84390.189

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