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- PDB-9erp: Hydrogenase-2 Ni-SI state -

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Basic information

Entry
Database: PDB / ID: 9erp
TitleHydrogenase-2 Ni-SI state
Components(Hydrogenase-2 ...) x 2
KeywordsOXIDOREDUCTASE / Hydrogenase / hydrogen
Function / homology
Function and homology information


hydrogenase (acceptor) / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding ...hydrogenase (acceptor) / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding / membrane / plasma membrane
Similarity search - Function
: / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenases large subunit signature 2. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit ...: / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenases large subunit signature 2. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / NICKEL (II) ION / IRON/SULFUR CLUSTER / Hydrogenase-2 large chain / Hydrogenase-2 small chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsCarr, S.B. / Li, W. / Wong, K.l. / Ash, P.A. / Vincent, K.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R018413/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X002624/1 United Kingdom
CitationJournal: To Be Published
Title: Glutamate flick enables proton tunnelling during fast redox biocatalysis
Authors: Carr, S.B. / Li, W. / Wong, K.l. / Evans, R.M. / Kendall-Price, S.E.T. / Ash, P.A. / Vincent, K.A.
History
DepositionMar 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: Hydrogenase-2 small chain
L: Hydrogenase-2 large chain
T: Hydrogenase-2 small chain
M: Hydrogenase-2 large chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,62021
Polymers189,8594
Non-polymers2,76117
Water23,4561302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24310 Å2
ΔGint-246 kcal/mol
Surface area44450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.180, 100.001, 167.814
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Hydrogenase-2 ... , 2 types, 4 molecules STLM

#1: Protein Hydrogenase-2 small chain / HYD2 / Membrane-bound hydrogenase 2 small subunit / NiFe hydrogenase


Mass: 32371.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Truncated construct with transmembrane helix removed
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hybO, yghV, b2997, JW2965 / Plasmid: pOC / Production host: Escherichia coli (E. coli) / Strain (production host): HJ001-hyp / References: UniProt: P69741, hydrogenase (acceptor)
#2: Protein Hydrogenase-2 large chain / HYD2 / Membrane-bound hydrogenase 2 large subunit / NiFe hydrogenase


Mass: 62557.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hybC, b2994, JW2962 / Plasmid: pOC / Production host: Escherichia coli (E. coli) / Strain (production host): HJ001-hyp / References: UniProt: P0ACE0, hydrogenase (acceptor)

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Non-polymers , 7 types, 1319 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2O / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1302 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100 mM bis tris pH 6 200 mM MgCl2 18-20% PEG 3350 / Temp details: Ambient temperature in anaerobic glove box

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.37→64.9 Å / Num. obs: 348218 / % possible obs: 100 % / Redundancy: 27.8 % / Biso Wilson estimate: 16.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.038 / Net I/σ(I): 9.7
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 28.5 % / Rmerge(I) obs: 3.72 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 17125 / CC1/2: 0.398 / Rpim(I) all: 0.398 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→64.28 Å / SU ML: 0.1966 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.0398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1742 17450 5.01 %
Rwork0.1565 330535 -
obs0.1574 347985 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.7 Å2
Refinement stepCycle: LAST / Resolution: 1.37→64.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12654 0 84 1302 14040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008713185
X-RAY DIFFRACTIONf_angle_d1.027918018
X-RAY DIFFRACTIONf_chiral_restr0.08341987
X-RAY DIFFRACTIONf_plane_restr0.00982332
X-RAY DIFFRACTIONf_dihedral_angle_d6.53131788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.36725480.35210794X-RAY DIFFRACTION98.96
1.39-1.40.36575810.351210912X-RAY DIFFRACTION99.85
1.4-1.420.34716280.337710870X-RAY DIFFRACTION99.92
1.42-1.440.31766330.320410912X-RAY DIFFRACTION99.98
1.44-1.460.33375920.321610890X-RAY DIFFRACTION99.95
1.46-1.480.30735790.294910956X-RAY DIFFRACTION99.95
1.48-1.50.27326390.271310877X-RAY DIFFRACTION99.97
1.5-1.520.27695540.256910968X-RAY DIFFRACTION99.91
1.52-1.540.24446050.234710942X-RAY DIFFRACTION99.97
1.54-1.570.22325800.222710957X-RAY DIFFRACTION99.99
1.57-1.590.23276160.213210894X-RAY DIFFRACTION99.98
1.59-1.620.22675320.200411035X-RAY DIFFRACTION99.97
1.62-1.660.20085910.190910985X-RAY DIFFRACTION100
1.66-1.690.19755740.184810909X-RAY DIFFRACTION100
1.69-1.730.20215510.182811047X-RAY DIFFRACTION99.99
1.73-1.770.20345630.173310988X-RAY DIFFRACTION99.98
1.77-1.810.17946040.169410947X-RAY DIFFRACTION99.97
1.81-1.860.1835670.152811015X-RAY DIFFRACTION99.99
1.86-1.910.15915250.145711054X-RAY DIFFRACTION99.99
1.91-1.980.16896000.143911010X-RAY DIFFRACTION100
1.98-2.050.14465070.135311111X-RAY DIFFRACTION100
2.05-2.130.15235880.132311005X-RAY DIFFRACTION100
2.13-2.220.1555970.126411020X-RAY DIFFRACTION100
2.22-2.340.14985530.128611093X-RAY DIFFRACTION100
2.34-2.490.14585630.124511095X-RAY DIFFRACTION100
2.49-2.680.14275830.123711096X-RAY DIFFRACTION100
2.68-2.950.1476190.126711100X-RAY DIFFRACTION100
2.95-3.380.16095960.135411168X-RAY DIFFRACTION100
3.38-4.260.13775790.12711271X-RAY DIFFRACTION100
4.26-64.280.15556030.147211614X-RAY DIFFRACTION99.89

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