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- PDB-9er7: Hydrogenase-1 Ni-SCO state -

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Basic information

Entry
Database: PDB / ID: 9er7
TitleHydrogenase-1 Ni-SCO state
Components(Hydrogenase-1 ...) x 2
KeywordsOXIDOREDUCTASE / Hydrogenase / hydrogen
Function / homology
Function and homology information


hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration ...hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / cellular response to starvation / outer membrane-bounded periplasmic space / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane / metal ion binding
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 2. / Nickel-dependent hydrogenases large subunit signature 1. / [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 2. / Nickel-dependent hydrogenases large subunit signature 1. / [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 / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / Hydrogenase-1 large chain / Hydrogenase-1 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 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-1 small chain
L: Hydrogenase-1 large chain
T: Hydrogenase-1 small chain
M: Hydrogenase-1 large chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,44326
Polymers191,4644
Non-polymers2,98022
Water24,1941343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25770 Å2
ΔGint-372 kcal/mol
Surface area46420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.790, 96.010, 182.790
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-1 ... , 2 types, 4 molecules STLM

#1: Protein Hydrogenase-1 small chain / HYD1 / Membrane-bound hydrogenase 1 small subunit / NiFe hydrogenase


Mass: 30980.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: FTH004 / Gene: hyaA, b0972, JW0954 / Production host: Escherichia coli (E. coli) / References: UniProt: P69739, hydrogenase (acceptor)
#2: Protein Hydrogenase-1 large chain / HYD1 / Membrane-bound hydrogenase 1 large subunit / NiFe hydrogenase


Mass: 64751.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: FTH004 / Gene: hyaB, b0973, JW0955 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACD8, hydrogenase (acceptor)

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Non-polymers , 11 types, 1365 molecules

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


Mass: 351.640 Da / Num. of mol.: 2 / 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-SF3 / FE4-S3 CLUSTER


Mass: 319.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2O
#9: 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
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1343 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM tris pH8 200 mM LiSO4 150 mM NaCl 19-21% PEG 3350
Temp details: Ambient teperature 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: May 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.4→66.2 Å / Num. obs: 322458 / % possible obs: 99.4 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.055 / Net I/σ(I): 6.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 14 % / Rmerge(I) obs: 3.24 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 217651 / CC1/2: 0.533 / Rpim(I) all: 0.63 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0425phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→66.197 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.754 / SU ML: 0.06 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.059
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1894 16191 5.021 %
Rwork0.1686 306267 -
all0.17 --
obs-322458 99.88 %
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: 18.372 Å2
Baniso -1Baniso -2Baniso -3
1--0.521 Å2-0 Å20 Å2
2--2.109 Å20 Å2
3----1.588 Å2
Refinement stepCycle: LAST / Resolution: 1.4→66.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13154 0 93 1343 14590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01213870
X-RAY DIFFRACTIONr_bond_other_d0.0020.01612779
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.80318941
X-RAY DIFFRACTIONr_angle_other_deg0.7541.75929471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48651762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.667593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.935102212
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.07410643
X-RAY DIFFRACTIONr_chiral_restr0.0920.22012
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023273
X-RAY DIFFRACTIONr_nbd_refined0.2290.23027
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.212384
X-RAY DIFFRACTIONr_nbtor_refined0.1810.26844
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.26810
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.21032
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.234
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.212
X-RAY DIFFRACTIONr_nbd_other0.2420.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.235
X-RAY DIFFRACTIONr_mcbond_it1.4131.8226862
X-RAY DIFFRACTIONr_mcbond_other1.411.8226861
X-RAY DIFFRACTIONr_mcangle_it1.8793.2738600
X-RAY DIFFRACTIONr_mcangle_other1.8793.2738601
X-RAY DIFFRACTIONr_scbond_it2.4282.0477008
X-RAY DIFFRACTIONr_scbond_other2.4182.0466995
X-RAY DIFFRACTIONr_scangle_it3.6653.65710269
X-RAY DIFFRACTIONr_scangle_other3.6513.65510252
X-RAY DIFFRACTIONr_lrange_it4.80319.40716322
X-RAY DIFFRACTIONr_lrange_other4.66718.30515988
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
1.4-1.4360.38812220.392222080.392236720.7720.77298.97770.39
1.436-1.4760.35511710.346218660.346231120.8710.87199.67550.339
1.476-1.5180.30811420.305212330.306223970.8930.89899.90180.293
1.518-1.5650.28210520.274207870.274218470.9150.92299.96340.257
1.565-1.6160.25910450.24201370.241211900.9390.94699.96220.221
1.616-1.6730.2399980.222194530.223204530.9560.95799.99020.2
1.673-1.7360.22210190.195187780.196198000.960.9799.98480.173
1.736-1.8070.2029920.174180340.176190260.9710.9781000.154
1.807-1.8870.198790.16174280.161183090.9760.98299.98910.141
1.887-1.9790.1848590.153166290.155174900.9780.98599.98860.136
1.979-2.0860.1758440.147158170.149166660.9810.98799.970.132
2.086-2.2130.1657950.138149770.139157730.9820.98899.99370.124
2.213-2.3650.1667180.129141540.131148730.9830.9999.99330.116
2.365-2.5550.1656840.131131420.132138290.9840.9999.97830.118
2.555-2.7980.1646730.14121400.141128140.9840.98899.99220.128
2.798-3.1280.1596300.143109790.144116100.9850.98899.99140.133
3.128-3.610.1825580.15397270.155102880.9810.98699.97080.146
3.61-4.4180.1494240.14283220.14287460.9870.9881000.137
4.418-6.2350.1663040.1565670.15168710.9860.9881000.146
6.235-66.1970.1641760.16938030.16939790.9830.9831000.163

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