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- PDB-6ehs: E. coli Hydrogenase-2 chemically reduced structure -

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Basic information

Entry
Database: PDB / ID: 6ehs
TitleE. coli Hydrogenase-2 chemically reduced structure
Components(Hydrogenase-2 ...) x 2
KeywordsOXIDOREDUCTASE / Hydrogen oxidation / Membrane protein / NiFe Hydrogenase
Function / homology
Function and homology information


hydrogenase (acceptor) / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding ...hydrogenase (acceptor) / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding / membrane / plasma membrane
Similarity search - Function
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa 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. ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa 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 / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / 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
DITHIONITE / FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / NICKEL (II) ION / IRON/SULFUR CLUSTER / hydrogenase (acceptor) / Hydrogenase-2 large chain / 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. / Evans, R.M. / Beaton, S.E. / 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
DepositionSep 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2May 2, 2018Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rpim_I_all
Revision 1.3May 9, 2018Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)190,30820
Polymers187,3604
Non-polymers2,94816
Water17,997999
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer of Heterodimer (2 copies of both large and small subunits)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24510 Å2
ΔGint-252 kcal/mol
Surface area45110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.885, 100.065, 168.801
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: 32631.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hybO, yghV, b2997, JW2965 / Production host: Escherichia coli (E. coli)
References: UniProt: P69741, UniProt: B7LGE4*PLUS, hydrogenase (acceptor)
#2: Protein Hydrogenase-2 large chain / HYD2 / Membrane-bound hydrogenase 2 large subunit / NiFe hydrogenase


Mass: 61048.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Oxidative damage of cys 548 was modeled as sulfenic acid (CSO)
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hybC, b2994, JW2962 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ACE0, UniProt: P0ACE1*PLUS, hydrogenase (acceptor)

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Non-polymers , 7 types, 1015 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-FCO / CARBONMONOXIDE-(DICYANO) IRON


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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-DTN / DITHIONITE


Mass: 128.128 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O4S2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 44.63 % / Description: Rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM Bis-tris pH 5.5 200 mM MgCl2 18-22% PEG 3350
PH range: 5.5-5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 22, 2017
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.5→99.89 Å / Num. obs: 269411 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.056 / Net I/σ(I): 11.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 12174 / CC1/2: 0.554 / Rpim(I) all: 0.8 / % possible all: 99.9

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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→86.08 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.642 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1633 13573 5 %RANDOM
Rwork0.12435 ---
obs0.12629 255708 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.112 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å2-0 Å2
2---0.26 Å20 Å2
3----0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.5→86.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12649 0 88 999 13736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01913106
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211814
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.93917888
X-RAY DIFFRACTIONr_angle_other_deg1.035327485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87851643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50424.45573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.824152056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2421558
X-RAY DIFFRACTIONr_chiral_restr0.1090.21965
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114600
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022568
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_it1.7791.8126560
X-RAY DIFFRACTIONr_mcbond_other1.781.8126559
X-RAY DIFFRACTIONr_mcangle_it2.0812.7278198
X-RAY DIFFRACTIONr_mcangle_other2.0812.7278199
X-RAY DIFFRACTIONr_scbond_it2.7582.1246546
X-RAY DIFFRACTIONr_scbond_other2.7322.126520
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0113.0629597
X-RAY DIFFRACTIONr_long_range_B_refined2.97222.90815093
X-RAY DIFFRACTIONr_long_range_B_other2.87522.61414870
X-RAY DIFFRACTIONr_rigid_bond_restr3.023324920
X-RAY DIFFRACTIONr_sphericity_free16.7855627
X-RAY DIFFRACTIONr_sphericity_bonded9.409524948
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 959 -
Rwork0.27 18832 -
obs--99.91 %

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