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- PDB-9er6: Hydrogenase-1 Ni-SI state -

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Basic information

Entry
Database: PDB / ID: 9er6
TitleHydrogenase-1 Ni-SI state
Components(Hydrogenase-1 ...) x 2
KeywordsOXIDOREDUCTASE / Hydrogenase / hydrogen
Function / homology
Function and homology information


hydrogen metabolic process / fermentation / anaerobic electron transport chain / hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration ...hydrogen metabolic process / fermentation / anaerobic electron transport chain / hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / 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 / metal ion binding / 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 / 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: 1.45 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

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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)194,61527
Polymers191,4644
Non-polymers3,15223
Water24,1941343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26300 Å2
ΔGint-419 kcal/mol
Surface area46030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.800, 96.188, 182.582
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 , 10 types, 1366 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.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / 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 / Feature type: SUBJECT OF INVESTIGATION
#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-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
#12: 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: 42.82 %
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 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: I04 / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.45→65.5 Å / Num. obs: 290992 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.08 / Net I/σ(I): 6.1
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 13 % / Rmerge(I) obs: 3.1 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 14287 / CC1/2: 0.447 / Rpim(I) all: 0.93 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
REFMAC5.8.0419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→65.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.775 / SU ML: 0.06 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1844 14253 4.901 %
Rwork0.1705 276554 -
all0.171 --
obs-290807 99.915 %
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: 14.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.473 Å20 Å20 Å2
2--1.777 Å2-0 Å2
3----1.304 Å2
Refinement stepCycle: LAST / Resolution: 1.45→65.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13145 0 100 1343 14588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01213811
X-RAY DIFFRACTIONr_bond_other_d0.0020.01612722
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.65618859
X-RAY DIFFRACTIONr_angle_other_deg0.7211.58129322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48551749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.696595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29102194
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.51710641
X-RAY DIFFRACTIONr_chiral_restr0.0830.22009
X-RAY DIFFRACTIONr_chiral_restr_other0.1670.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023270
X-RAY DIFFRACTIONr_nbd_refined0.2190.22888
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.212290
X-RAY DIFFRACTIONr_nbtor_refined0.1780.26819
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.26805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.21031
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0210.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.234
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0670.28
X-RAY DIFFRACTIONr_nbd_other0.1970.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.231
X-RAY DIFFRACTIONr_mcbond_it1.1741.4266820
X-RAY DIFFRACTIONr_mcbond_other1.1741.4266820
X-RAY DIFFRACTIONr_mcangle_it1.6342.5648537
X-RAY DIFFRACTIONr_mcangle_other1.6342.5648538
X-RAY DIFFRACTIONr_scbond_it2.2491.6486991
X-RAY DIFFRACTIONr_scbond_other2.2371.6466970
X-RAY DIFFRACTIONr_scangle_it3.4182.92510248
X-RAY DIFFRACTIONr_scangle_other3.4072.9210219
X-RAY DIFFRACTIONr_lrange_it4.47915.24516079
X-RAY DIFFRACTIONr_lrange_other4.3314.2915756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.4880.31210220.31120315X-RAY DIFFRACTION99.6963
1.488-1.5280.3089960.29719759X-RAY DIFFRACTION99.7789
1.528-1.5730.2829140.27519253X-RAY DIFFRACTION99.8218
1.573-1.6210.269700.25618692X-RAY DIFFRACTION99.8324
1.621-1.6740.2489690.23818084X-RAY DIFFRACTION99.8847
1.674-1.7330.2269230.21417503X-RAY DIFFRACTION99.9078
1.733-1.7980.2119420.19716907X-RAY DIFFRACTION99.9608
1.798-1.8720.1958060.18116350X-RAY DIFFRACTION99.965
1.872-1.9550.1777500.16315767X-RAY DIFFRACTION99.9637
1.955-2.050.1797030.15315051X-RAY DIFFRACTION99.9873
2.05-2.1610.1677930.14214223X-RAY DIFFRACTION99.9933
2.161-2.2920.1577580.13413510X-RAY DIFFRACTION99.993
2.292-2.450.1516650.12812708X-RAY DIFFRACTION100
2.45-2.6460.166060.13211894X-RAY DIFFRACTION100
2.646-2.8980.166060.13610913X-RAY DIFFRACTION99.9913
2.898-3.2390.1624850.149980X-RAY DIFFRACTION100
3.239-3.7390.1554800.1488816X-RAY DIFFRACTION100
3.739-4.5750.143660.1357535X-RAY DIFFRACTION100
4.575-6.4550.1682750.1645925X-RAY DIFFRACTION100
6.455-65.50.1752240.1763369X-RAY DIFFRACTION100

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