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- PDB-8ru6: Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both ... -

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Basic information

Entry
Database: PDB / ID: 8ru6
TitleDesulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 4 amino acid linker peptide derived from CpI of Clostridium pasteurianum
ComponentsPeriplasmic [Fe] hydrogenase large subunit,CpI,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 1-like, iron-sulfur centre-binding domain / 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, small subunit HydB-type / : / Iron hydrogenase 1-like, iron-sulfur centre-binding domain / 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 / 2Fe-2S iron-sulfur cluster binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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-MHX / IRON/SULFUR CLUSTER / Periplasmic [Fe] hydrogenase large subunit / Periplasmic [Fe] hydrogenase small subunit / Iron hydrogenase 1
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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
DepositionJan 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,4959
Polymers54,2801
Non-polymers2,2158
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-48 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.397, 88.857, 106.592
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 54280.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: hydA, DVU_1769, hydB, DVU_1770 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): (delta)iscR
References: UniProt: P07598, UniProt: P29166, UniProt: P07603, ferredoxin hydrogenase
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: 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
#4: Chemical ChemComp-MHX / Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form)


Mass: 382.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5Fe2N3O4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.2 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: 0.77486 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: 0.77486 Å / Relative weight: 1
ReflectionResolution: 1.15→45.747 Å / Num. obs: 166648 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 1 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.042 / Rrim(I) all: 0.111 / Χ2: 1.02 / Net I/σ(I): 15.4
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.834 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8168 / CC1/2: 0.621 / Rpim(I) all: 0.806 / Rrim(I) all: 2.007 / Χ2: 1.04 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Cootmodel building
REFMAC5.8.0425refinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→45.747 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.184 / SU ML: 0.023 / Cross valid method: NONE / ESU R: 0.031 / ESU R Free: 0.031
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1582 8364 5.022 %
Rwork0.1367 158184 -
all0.138 --
obs-166548 99.908 %
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: 13.754 Å2
Baniso -1Baniso -2Baniso -3
1--0.124 Å2-0 Å2-0 Å2
2---0.55 Å20 Å2
3---0.673 Å2
Refinement stepCycle: LAST / Resolution: 1.15→45.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3737 0 85 480 4302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124000
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163714
X-RAY DIFFRACTIONr_angle_refined_deg2.1121.8575434
X-RAY DIFFRACTIONr_angle_other_deg0.6961.7718661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4465501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.895515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39110676
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.3610158
X-RAY DIFFRACTIONr_chiral_restr0.1590.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02812
X-RAY DIFFRACTIONr_nbd_refined0.2360.2815
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.23460
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21947
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21974
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2322
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0340.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.217
X-RAY DIFFRACTIONr_nbd_other0.3010.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2180.241
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0060.21
X-RAY DIFFRACTIONr_mcbond_it3.6261.3041957
X-RAY DIFFRACTIONr_mcbond_other3.6161.3041956
X-RAY DIFFRACTIONr_mcangle_it5.0322.3522449
X-RAY DIFFRACTIONr_mcangle_other5.0412.3542450
X-RAY DIFFRACTIONr_scbond_it5.4381.5522043
X-RAY DIFFRACTIONr_scbond_other5.4491.5512032
X-RAY DIFFRACTIONr_scangle_it7.5962.7272936
X-RAY DIFFRACTIONr_scangle_other7.6072.7232925
X-RAY DIFFRACTIONr_lrange_it10.90517.3584621
X-RAY DIFFRACTIONr_lrange_other10.90617.3594620
X-RAY DIFFRACTIONr_rigid_bond_restr3.60537714
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
1.15-1.180.2536320.244115180.244121800.9470.94999.75370.236
1.18-1.2120.2336250.218112570.219118880.9550.95999.94950.207
1.212-1.2470.2215840.208109730.209115580.960.96499.99130.194
1.247-1.2860.2195630.192106860.193112500.9640.9799.99110.176
1.286-1.3280.2095540.179103830.18109370.9650.9751000.16
1.328-1.3740.1765420.16100490.161105930.9770.9899.98110.14
1.374-1.4260.1685110.1496310.142101430.9790.98599.99010.12
1.426-1.4840.1565040.12293390.12498450.9820.98999.97970.101
1.484-1.550.1375070.10889080.10994410.9870.99299.72460.088
1.55-1.6260.1234310.09185650.09389960.990.9941000.074
1.626-1.7140.1224270.08682070.08886340.9910.9951000.073
1.714-1.8180.1283780.09277930.09381710.990.9941000.079
1.818-1.9430.1273810.09472750.09676560.990.9941000.083
1.943-2.0980.1393690.11167990.11271680.9870.9921000.099
2.098-2.2980.1473500.11162590.11366090.9870.9921000.102
2.298-2.5680.1312930.11457170.11560100.9890.9921000.106
2.568-2.9640.152700.13650330.13753380.9860.98899.34430.129
2.964-3.6270.1791920.16443530.16545450.9820.9851000.162
3.627-5.1130.1521600.14934280.14935880.9870.9871000.153
5.113-45.7470.184910.17920110.17921030.9830.9899.95240.186

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