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- PDB-6en9: E. coli Hydrogenase-2 (hydrogen reduced form) -

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Basic information

Entry
Database: PDB / ID: 6en9
TitleE. coli Hydrogenase-2 (hydrogen reduced form)
Components(Hydrogenase-2 ...) x 2
KeywordsOXIDOREDUCTASE / NiFe Hydrogenase / membrane protein / hydrogen oxidation
Function / homology
Function and homology information


[Ni-Fe] hydrogenase complex / hydrogenase (acceptor) / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / anaerobic respiration / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding ...[Ni-Fe] hydrogenase complex / hydrogenase (acceptor) / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / anaerobic respiration / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / membrane / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [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. ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [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 / Few Secondary Structures / Irregular / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
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: 1.5 Å
AuthorsCarr, S.B. / Beaton, S.E. / Evans, R.M. / Armstrong, F.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N006321/1 United Kingdom
CitationJournal: Biochem. J. / Year: 2018
Title: The structure of hydrogenase-2 fromEscherichia coli: implications for H2-driven proton pumping.
Authors: Beaton, S.E. / Evans, R.M. / Finney, A.J. / Lamont, C.M. / Armstrong, F.A. / Sargent, F. / Carr, S.B.
History
DepositionOct 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)192,48718
Polymers189,8594
Non-polymers2,62814
Water20,0511113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23570 Å2
ΔGint-276 kcal/mol
Surface area44900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.602, 100.540, 168.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hybO, yghV, b2997, JW2965 / Production host: Escherichia coli (E. coli) / 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) / References: UniProt: P0ACE0, hydrogenase (acceptor)

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Non-polymers , 7 types, 1127 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Fe4S4
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2O
#7: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1113 / Source method: isolated from a natural source / Formula: H2O

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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: 44.66 % / Description: Very long rods
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 100 mM Bis-tris pH 5.5-5.9, 18-22 % (w/v) PEG 3350, 200 mM MgCl2
PH range: 5.5-5.9 / Temp details: crystallised in anaerobic chamber

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→168.59 Å / Num. obs: 267144 / % possible obs: 99.2 % / Redundancy: 5.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.039 / Rrim(I) all: 0.09 / Net I/σ(I): 10.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 13008 / CC1/2: 0.714 / Rpim(I) all: 0.439 / Rrim(I) all: 1.053 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ehq

6ehq


Resolution: 1.5→86.35 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.298 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.063 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17502 13461 5 %RANDOM
Rwork0.15199 ---
obs0.15313 253537 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.211 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--0.18 Å2-0 Å2
3----0.97 Å2
Refinement stepCycle: 1 / Resolution: 1.5→86.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12640 0 74 1113 13827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01913135
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211841
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.93817942
X-RAY DIFFRACTIONr_angle_other_deg1.071327560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16651655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96424.498578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.842152065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.551558
X-RAY DIFFRACTIONr_chiral_restr0.1180.21966
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02114669
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022575
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4071.7946575
X-RAY DIFFRACTIONr_mcbond_other1.4071.7946574
X-RAY DIFFRACTIONr_mcangle_it1.8962.6888221
X-RAY DIFFRACTIONr_mcangle_other1.8962.6888222
X-RAY DIFFRACTIONr_scbond_it2.3161.9996560
X-RAY DIFFRACTIONr_scbond_other2.3131.9956546
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4762.9099635
X-RAY DIFFRACTIONr_long_range_B_refined4.3522.32415269
X-RAY DIFFRACTIONr_long_range_B_other4.2522.01715012
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 958 -
Rwork0.248 18445 -
obs--98.1 %

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