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- PDB-8ryh: Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both ... -

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Basic information

Entry
Database: PDB / ID: 8ryh
TitleDesulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a linker peptide derived from a group A1 type [FeFe]-hydrogenase of Veillonella atypica
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: 1.773 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
DepositionFeb 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4675
Polymers54,0571
Non-polymers1,4104
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.118, 50.603, 86.643
Angle α, β, γ (deg.)90, 105.331, 90
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 54056.957 Da / Num. of mol.: 1
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-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 1 M Lithium chloride, 0.1 M Sodium acetate, 25 % Polyethylene glycol 4000

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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: Aug 28, 2023
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: 1.77→45.402 Å / Num. obs: 41648 / % possible obs: 96.4 % / Redundancy: 6.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.098 / Rrim(I) all: 0.187 / Χ2: 1 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.04-45.366.30.05426.43610.9950.0340.0640.9999.4
1.77-1.8171.0582.313790.7260.6461.242155.8

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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: 1.773→45.402 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.201 / SU B: 3.102 / SU ML: 0.099 / Average fsc free: 0.9603 / Average fsc work: 0.9724 / Cross valid method: NONE / ESU R: 0.147 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2461 2085 5.006 %
Rwork0.2048 39562 -
all0.207 --
obs-41647 96.311 %
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: 20.573 Å2
Baniso -1Baniso -2Baniso -3
1-0.903 Å2-0 Å2-0.719 Å2
2---1.054 Å2-0 Å2
3---0.473 Å2
Refinement stepCycle: LAST / Resolution: 1.773→45.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 0 41 117 3760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123770
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163481
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.8485136
X-RAY DIFFRACTIONr_angle_other_deg0.5691.7728095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7215473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.625517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0810633
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.29110152
X-RAY DIFFRACTIONr_chiral_restr0.0980.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
X-RAY DIFFRACTIONr_nbd_refined0.2230.2831
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.23282
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21839
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2168
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.030.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1160.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.212
X-RAY DIFFRACTIONr_nbd_other0.1950.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.25
X-RAY DIFFRACTIONr_mcbond_it1.6011.9431880
X-RAY DIFFRACTIONr_mcbond_other1.61.9431880
X-RAY DIFFRACTIONr_mcangle_it2.3643.4852348
X-RAY DIFFRACTIONr_mcangle_other2.3653.4862349
X-RAY DIFFRACTIONr_scbond_it1.922.1241890
X-RAY DIFFRACTIONr_scbond_other1.922.1231891
X-RAY DIFFRACTIONr_scangle_it2.9813.8142744
X-RAY DIFFRACTIONr_scangle_other2.983.8142745
X-RAY DIFFRACTIONr_lrange_it4.21918.84258
X-RAY DIFFRACTIONr_lrange_other4.21218.6914248
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
1.773-1.8190.281920.24320080.24531810.9420.95566.0170.234
1.819-1.8690.2391450.22229000.22330640.9590.96599.37990.211
1.869-1.9230.2331430.2128600.21130350.9620.96998.94560.197
1.923-1.9820.2531320.20527500.20729030.9560.97199.27660.19
1.982-2.0470.2581490.20626210.20928350.9540.9797.70720.187
2.047-2.1190.2641360.19924830.20227620.9510.97394.82260.18
2.119-2.1990.2591330.18124860.18426360.9610.97999.35510.165
2.199-2.2880.2371360.17923960.18225490.9670.9899.33310.163
2.288-2.390.2231060.17923220.1824430.9660.9899.3860.164
2.39-2.5060.2421170.18722140.18923450.9640.97899.4030.173
2.506-2.6410.2531190.18921150.19322450.9610.97799.510.176
2.641-2.8010.2441220.19519910.19821240.9620.97699.48210.183
2.801-2.9940.258940.20118680.20419680.9580.97499.69510.191
2.994-3.2320.269860.21817630.2218540.9480.96799.73030.21
3.232-3.5390.251800.21416270.21617160.9620.97299.47550.21
3.539-3.9540.214800.19613630.19715500.9730.97893.09680.199
3.954-4.5590.222810.20312890.20413860.9780.97798.84560.215
4.559-5.570.244490.22311230.22411730.970.9799.91470.238
5.57-7.8190.261550.2378620.2389190.9590.96499.78240.248
7.819-45.4020.268300.2395210.2415510.9760.9721000.252

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