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- PDB-9era: Hydrogenase-1 Ni-Lii state -

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Basic information

Entry
Database: PDB / ID: 9era
TitleHydrogenase-1 Ni-Lii 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 / ferredoxin hydrogenase complex / [Ni-Fe] 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 / ferredoxin hydrogenase complex / [Ni-Fe] 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 / 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 / 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 / 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: 1.65 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-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)194,07321
Polymers191,4644
Non-polymers2,61017
Water11,818656
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24850 Å2
ΔGint-334 kcal/mol
Surface area46270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.679, 97.072, 183.149
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:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSARGARGSA4 - 2664 - 266
211LYSLYSARGARGTC4 - 2664 - 266
322SERSERHISHISLB2 - 5822 - 582
422SERSERHISHISMD2 - 5822 - 582

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-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) / Strain (production host): FTH004 / 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) / Gene: hyaB, b0973, JW0955 / Production host: Escherichia coli (E. coli) / Strain (production host): FTH004 / References: UniProt: P0ACD8, hydrogenase (acceptor)

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Non-polymers , 9 types, 673 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-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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM Tris 200 mM Li2SO4 150 mM NaCl 20% PEG 3350 / Temp details: ambient temperature in an anaerobic glovebox

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8153 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8153 Å / Relative weight: 1
ReflectionResolution: 1.65→54.3 Å / Num. obs: 200470 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.99 / Rmerge(I) obs: 0.419 / Rpim(I) all: 0.116 / Net I/σ(I): 4.5
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 14.4 % / Rmerge(I) obs: 3.46 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 9808 / CC1/2: 0.445 / Rpim(I) all: 0.941 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→54.287 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.88 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.111 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2222 10041 5.009 %
Rwork0.2041 190429 -
all0.205 --
obs-200470 99.991 %
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: 19.601 Å2
Baniso -1Baniso -2Baniso -3
1--0.162 Å20 Å2-0 Å2
2--1.976 Å20 Å2
3----1.814 Å2
Refinement stepCycle: LAST / Resolution: 1.65→54.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13154 0 71 656 13881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01213885
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612814
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.64818984
X-RAY DIFFRACTIONr_angle_other_deg0.6231.57129570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58751780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.163591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.288102224
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.71610646
X-RAY DIFFRACTIONr_chiral_restr0.0640.22025
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216564
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023280
X-RAY DIFFRACTIONr_nbd_refined0.210.22905
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.212514
X-RAY DIFFRACTIONr_nbtor_refined0.1760.26761
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.26841
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2697
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0510.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.235
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.212
X-RAY DIFFRACTIONr_nbd_other0.230.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.213
X-RAY DIFFRACTIONr_mcbond_it1.1221.9356862
X-RAY DIFFRACTIONr_mcbond_other1.1221.9356862
X-RAY DIFFRACTIONr_mcangle_it1.6873.488602
X-RAY DIFFRACTIONr_mcangle_other1.6873.488603
X-RAY DIFFRACTIONr_scbond_it1.8112.1257023
X-RAY DIFFRACTIONr_scbond_other1.8112.1257014
X-RAY DIFFRACTIONr_scangle_it2.9063.82210296
X-RAY DIFFRACTIONr_scangle_other2.9073.8210285
X-RAY DIFFRACTIONr_lrange_it3.71518.83716011
X-RAY DIFFRACTIONr_lrange_other3.70918.59915912
X-RAY DIFFRACTIONr_ncsr_local_group_10.0590.058786
X-RAY DIFFRACTIONr_ncsr_local_group_20.0560.0520448
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11SX-RAY DIFFRACTIONLocal ncs0.059150.0501
12SX-RAY DIFFRACTIONLocal ncs0.059150.0501
23SX-RAY DIFFRACTIONLocal ncs0.055820.05009
24SX-RAY DIFFRACTIONLocal ncs0.055820.05009
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
1.65-1.6930.4077810.408138630.408146540.7540.75699.93180.407
1.693-1.7390.3797220.386136070.386143300.8660.86299.9930.386
1.739-1.790.3596730.363132630.363139360.8830.8761000.363
1.79-1.8450.3635960.331129190.332135160.8750.89399.99260.33
1.845-1.9050.3156220.303125170.304131390.8930.9041000.3
1.905-1.9720.2766410.272120390.272126800.9320.9321000.265
1.972-2.0460.2666250.243116450.244122700.9420.9491000.232
2.046-2.1290.2285970.218112510.218118480.9580.9631000.203
2.129-2.2240.2225520.202107690.203113210.9640.971000.186
2.224-2.3320.2075660.185102930.186108590.970.9751000.166
2.332-2.4580.1964830.17698720.177103550.9720.9791000.157
2.458-2.6070.2054340.16593840.16698180.9740.9821000.143
2.607-2.7870.2035000.16787000.16892000.9720.9821000.145
2.787-3.0090.1784430.15781860.15886290.9790.9841000.137
3.009-3.2950.1874080.15775550.15979630.9780.9851000.14
3.295-3.6830.1763980.15468010.15571990.9820.9861000.14
3.683-4.2490.1643310.14360900.14464210.9820.9871000.131
4.249-5.1960.172950.14151600.14354550.9850.9891000.134
5.196-7.3150.2052440.17240560.17443000.9830.9861000.16
7.315-54.2870.141250.16424060.16325310.9880.9831000.162

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