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- PDB-6ehq: E. coli Hydrogenase-2 (as isolated form). -

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Basic information

Entry
Database: PDB / ID: 6ehq
TitleE. coli Hydrogenase-2 (as isolated 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: 2.2 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
DepositionSep 14, 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 2.0Jul 11, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
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.auth_seq_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_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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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)189,76416
Polymers187,3284
Non-polymers2,43612
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23320 Å2
ΔGint-248 kcal/mol
Surface area45360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.064, 100.090, 168.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11S
21T
12L
22M

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010S7 - 272
2010T7 - 272
1020L2 - 552
2020M2 - 552

NCS ensembles :
ID
1
2

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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, hydrogenase (acceptor)
#2: Protein Hydrogenase-2 large chain / HYD2 / Membrane-bound hydrogenase 2 large subunit / NiFe hydrogenase


Mass: 61032.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hybC, b2994, JW2962 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACE0, hydrogenase (acceptor)

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Non-polymers , 6 types, 537 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-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 / Nickel


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.19 Å3/Da / Density % sol: 43.96 % / 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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→86 Å / Num. obs: 93703 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / CC1/2: 0.978 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.12 / Net I/σ(I): 6.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4242 / CC1/2: 0.68 / Rpim(I) all: 0.63 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A4M

5a4m


Resolution: 2.2→86 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 11.05 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18951 4141 4.9 %RANDOM
Rwork0.16231 ---
obs0.16365 79987 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.825 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å20 Å2
2--0.55 Å2-0 Å2
3----1.5 Å2
Refinement stepCycle: 1 / Resolution: 2.2→86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12647 0 64 525 13236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213058
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211795
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.93817809
X-RAY DIFFRACTIONr_angle_other_deg1.01327434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98851635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16524.45573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.507152053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6121558
X-RAY DIFFRACTIONr_chiral_restr0.0920.21952
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022561
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_it1.1372.6426549
X-RAY DIFFRACTIONr_mcbond_other1.1372.6426548
X-RAY DIFFRACTIONr_mcangle_it1.8313.9578181
X-RAY DIFFRACTIONr_mcangle_other1.8313.9578182
X-RAY DIFFRACTIONr_scbond_it1.6672.8316509
X-RAY DIFFRACTIONr_scbond_other1.6672.8316503
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.764.1689574
X-RAY DIFFRACTIONr_long_range_B_refined3.77531.49714763
X-RAY DIFFRACTIONr_long_range_B_other3.74731.42514675
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11S168400.04
12T168400.04
21L375440.05
22M375440.05
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 277 -
Rwork0.276 5665 -
obs--95.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0765-0.0393-0.08570.1381-0.08420.23920.007-0.01880.01490.0185-0.0199-0.0319-0.04030.05220.01290.0178-0.0126-0.00980.0395-0.00160.0136107.3151114.679719.7449
20.16580.0334-0.06330.16510.10450.26240.02290.0566-0.0005-0.0099-0.00540.016-0.0368-0.0598-0.01760.01320.0093-0.00280.0618-0.00150.011990.0193110.5121-17.0786
30.0983-0.0787-0.00340.2058-0.03420.1991-0.0135-0.0057-0.02050.01720.00380.02050.0195-0.01150.00970.0128-0.00090.00380.0210.00590.006490.329999.009427.9332
40.12070.0974-0.09510.1361-0.02490.3299-0.02440.0245-0.0217-0.0134-0.005-0.02050.0632-0.00630.02930.02360.00290.00260.0347-0.01090.0134107.15793.5919-21.7302
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1S10 - 403
2X-RAY DIFFRACTION2T9 - 403
3X-RAY DIFFRACTION3L2 - 603
4X-RAY DIFFRACTION4M2 - 603

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