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- PDB-9err: Hydrogenase-2 Ni-SCO state -

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Basic information

Entry
Database: PDB / ID: 9err
TitleHydrogenase-2 Ni-SCO 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
CARBON MONOXIDE / 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: 1.4 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)192,60823
Polymers189,8594
Non-polymers2,74919
Water20,6811148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24630 Å2
ΔGint-275 kcal/mol
Surface area44800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.185, 99.755, 168.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 deleted
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 , 8 types, 1167 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.: 2 / 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.: 5 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1148 / 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: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100mM bistris 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: 1.4→64.5 Å / Num. obs: 330212 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.076 / Net I/σ(I): 6.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 14 % / Rmerge(I) obs: 2.69 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 16168 / CC1/2: 0.438 / Rpim(I) all: 0.77 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
REFMAC5.8.0419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→64.5 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.292 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.055
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1809 16420 4.976 %
Rwork0.1608 313539 -
all0.162 --
obs-329959 99.925 %
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: 13.605 Å2
Baniso -1Baniso -2Baniso -3
1-0.422 Å20 Å20 Å2
2--0.14 Å2-0 Å2
3----0.562 Å2
Refinement stepCycle: LAST / Resolution: 1.4→64.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12670 0 83 1148 13901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01213230
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612213
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.65618084
X-RAY DIFFRACTIONr_angle_other_deg0.5661.5828207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47551673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.686560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.303102089
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.77610586
X-RAY DIFFRACTIONr_chiral_restr0.0880.21979
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215655
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022929
X-RAY DIFFRACTIONr_nbd_refined0.2290.22816
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.211836
X-RAY DIFFRACTIONr_nbtor_refined0.180.26556
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.26463
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2874
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1690.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.232
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2790.29
X-RAY DIFFRACTIONr_nbd_other0.2030.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2730.219
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0450.21
X-RAY DIFFRACTIONr_mcbond_it1.2131.3256614
X-RAY DIFFRACTIONr_mcbond_other1.2121.3256613
X-RAY DIFFRACTIONr_mcangle_it1.6652.388274
X-RAY DIFFRACTIONr_mcangle_other1.6652.3798275
X-RAY DIFFRACTIONr_scbond_it2.2691.5216616
X-RAY DIFFRACTIONr_scbond_other2.271.5216611
X-RAY DIFFRACTIONr_scangle_it3.4982.6959737
X-RAY DIFFRACTIONr_scangle_other3.4982.6969732
X-RAY DIFFRACTIONr_lrange_it4.11613.4415232
X-RAY DIFFRACTIONr_lrange_other4.06413.12414997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.29612640.29722876X-RAY DIFFRACTION99.8676
1.436-1.4760.28911820.28222451X-RAY DIFFRACTION99.9197
1.476-1.5180.26811010.25621877X-RAY DIFFRACTION99.9348
1.518-1.5650.24510580.23721206X-RAY DIFFRACTION99.9327
1.565-1.6160.23710100.21420638X-RAY DIFFRACTION99.9538
1.616-1.6730.21810450.19919873X-RAY DIFFRACTION99.957
1.673-1.7360.2110240.18719218X-RAY DIFFRACTION99.9753
1.736-1.8070.2079190.1718563X-RAY DIFFRACTION99.959
1.807-1.8870.1839390.15817790X-RAY DIFFRACTION99.9626
1.887-1.9790.1798980.14816961X-RAY DIFFRACTION99.9888
1.979-2.0860.1678540.14316226X-RAY DIFFRACTION99.9883
2.086-2.2130.1567880.13315356X-RAY DIFFRACTION100
2.213-2.3650.1627400.1314433X-RAY DIFFRACTION100
2.365-2.5550.1447360.12213444X-RAY DIFFRACTION99.9859
2.555-2.7980.1457130.12412356X-RAY DIFFRACTION100
2.798-3.1280.1615950.13711280X-RAY DIFFRACTION100
3.128-3.610.1615380.1459981X-RAY DIFFRACTION100
3.61-4.4180.1424450.1268497X-RAY DIFFRACTION99.9776
4.418-6.2330.1743570.1446675X-RAY DIFFRACTION100
6.233-64.50.1592140.1723839X-RAY DIFFRACTION99.926

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