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- PDB-9erc: Hydrogenase-2 Ni-Li state -

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Basic information

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


hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding ...hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / nickel cation 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 / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / : / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / 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 / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / : / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / 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: 1.308 Å
AuthorsWong, K.L. / Carr, S.B. / 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 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 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)193,82237
Polymers189,8594
Non-polymers3,96333
Water24,2121344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28130 Å2
ΔGint-285 kcal/mol
Surface area43570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.877, 99.974, 168.071
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11S
21T
32L
42M

NCS domain segments:

Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: VAL / End label comp-ID: VAL

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SA10 - 2759 - 274
211TC10 - 2759 - 274
322LB3 - 5513 - 551
422MD3 - 5513 - 551

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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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
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 / Production host: Escherichia coli (E. coli) / Strain (production host): HJ001-hyp / References: UniProt: P0ACE0, hydrogenase (acceptor)

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Non-polymers , 7 types, 1377 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.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#7: 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
#8: 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
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1344 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100 mM BisTris 200 mM MgCl2 20% PEG 3350
Temp details: Ambient temperature inside an anaerobic glovebox

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.308→100 Å / Num. obs: 402048 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.06 / Net I/σ(I): 5.8
Reflection shellResolution: 1.31→1.33 Å / Redundancy: 14 % / Rmerge(I) obs: 3.78 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 19627 / CC1/2: 0.313 / Rpim(I) all: 1.04 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.308→86.07 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.797 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.049
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.193 1979 0.505 %
Rwork0.1739 390097 -
all0.174 --
obs-392076 97.452 %
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: 16.634 Å2
Baniso -1Baniso -2Baniso -3
1-0.019 Å20 Å2-0 Å2
2--0.643 Å20 Å2
3----0.663 Å2
Refinement stepCycle: LAST / Resolution: 1.308→86.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12639 0 160 1344 14143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01213339
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612319
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.65218223
X-RAY DIFFRACTIONr_angle_other_deg0.5311.57328460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24951686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.76558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.399102092
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.74610585
X-RAY DIFFRACTIONr_chiral_restr0.0810.21999
X-RAY DIFFRACTIONr_chiral_restr_other0.0070.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022950
X-RAY DIFFRACTIONr_nbd_refined0.2230.22887
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.212474
X-RAY DIFFRACTIONr_nbtor_refined0.1810.26652
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.26916
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.21126
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1460.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.230
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.214
X-RAY DIFFRACTIONr_nbd_other0.1870.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2020.222
X-RAY DIFFRACTIONr_mcbond_it1.2751.6246651
X-RAY DIFFRACTIONr_mcbond_other1.2741.6246650
X-RAY DIFFRACTIONr_mcangle_it1.7512.9158341
X-RAY DIFFRACTIONr_mcangle_other1.7512.9158342
X-RAY DIFFRACTIONr_scbond_it2.581.8776688
X-RAY DIFFRACTIONr_scbond_other2.581.8776689
X-RAY DIFFRACTIONr_scangle_it3.9883.3169813
X-RAY DIFFRACTIONr_scangle_other3.9883.3169814
X-RAY DIFFRACTIONr_lrange_it5.07217.16115786
X-RAY DIFFRACTIONr_lrange_other5.07217.11315782
X-RAY DIFFRACTIONr_ncsr_local_group_10.060.058684
X-RAY DIFFRACTIONr_ncsr_local_group_20.0530.0519343
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11SX-RAY DIFFRACTIONLocal ncs0.060220.0501
12SX-RAY DIFFRACTIONLocal ncs0.060220.0501
23SX-RAY DIFFRACTIONLocal ncs0.053140.0501
24SX-RAY DIFFRACTIONLocal ncs0.053140.0501
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
1.308-1.3420.3511200.401213510.401295140.8860.86872.74850.398
1.342-1.3790.3831360.386265920.386288040.890.87892.79270.384
1.379-1.4190.3671610.372277620.372280480.8950.8999.55430.371
1.419-1.4630.2961260.351270980.351272290.9210.90299.98160.352
1.463-1.5110.3251190.319263260.319264460.9250.91999.99620.322
1.511-1.5640.2691490.283254070.283255570.9490.93699.99610.285
1.564-1.6230.2511150.251244960.251246110.9540.9531000.248
1.623-1.6890.2191250.216236450.216237700.9650.9661000.207
1.689-1.7640.2181020.196226850.196227870.9710.9741000.18
1.764-1.850.1931310.172217300.172218610.9750.981000.153
1.85-1.950.1981050.161206380.161207430.9750.9831000.143
1.95-2.0680.181940.154195980.155196920.9830.9861000.138
2.068-2.2110.178860.143184260.143185120.9820.9891000.127
2.211-2.3880.173720.134172130.134172850.9830.991000.117
2.388-2.6160.133800.123158410.123159210.9880.9911000.105
2.616-2.9240.179780.122143530.123144310.9810.9911000.104
2.924-3.3760.137640.122127430.122128070.9890.9911000.106
3.376-4.1330.135530.113108230.113108760.9890.9921000.102
4.133-5.8380.158490.1384850.1385340.990.9931000.122
5.838-86.070.145140.18448860.18449000.9880.9761000.179

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