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- PDB-6fpo: High resolution structure of native Hydrogenase (Hyd-1) -

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Basic information

Entry
Database: PDB / ID: 6fpo
TitleHigh resolution structure of native Hydrogenase (Hyd-1)
Components(Hydrogenase-1 ...) x 2
KeywordsOXIDOREDUCTASE / NiFe hydrogenase / Iron sulphur cluster / periplasm / 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 / 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
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 CFT073 (bacteria)
Escherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsCarr, S.B. / Armstrong, F.A. / Evans, R.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N006321/1 United Kingdom
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Mechanistic Exploitation of a Self-Repairing, Blocked Proton Transfer Pathway in an O2-Tolerant [NiFe]-Hydrogenase.
Authors: Evans, R.M. / Ash, P.A. / Beaton, S.E. / Brooke, E.J. / Vincent, K.A. / Carr, S.B. / Armstrong, F.A.
History
DepositionFeb 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 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 / struct_conn_type
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)206,82723
Polymers203,1644
Non-polymers3,66319
Water31,4901748
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26170 Å2
ΔGint-311 kcal/mol
Surface area46650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.786, 97.733, 183.102
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-1 ... , 2 types, 4 molecules STLM

#1: Protein Hydrogenase-1 small chain / HYD1 / Membrane-bound hydrogenase 1 small subunit / NiFe hydrogenase


Mass: 36814.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli CFT073 (bacteria) / Gene: hyaA, c1113 / Variant: FTH004 / Production host: Escherichia coli CFT073 (bacteria) / References: UniProt: P69740, hydrogenase (acceptor)
#2: Protein Hydrogenase-1 large chain / HYD1 / Membrane-bound hydrogenase 1 large subunit / NiFe hydrogenase


Mass: 64767.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / Variant: FTH004 / References: UniProt: P0ACD8, hydrogenase (acceptor)

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Sugars , 1 types, 2 molecules

#6: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 10 types, 1765 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
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#12: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1748 / 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: 2.1 Å3/Da / Density % sol: 46.4 % / Description: Rods with rectangular cross-section
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 100 mM tris pH 8.1 200 mM LiSO4 150 mM NaCl 20-22% PEG 3350
PH range: 8.0-8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.05→99.55 Å / Num. obs: 773665 / % possible obs: 99.8 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.3
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 11.3 % / Rmerge(I) obs: 2.21 / Mean I/σ(I) obs: 1.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4USC

4usc


Resolution: 1.05→91.55 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.754 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.021 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.134 38607 5 %RANDOM
Rwork0.115 ---
obs0.116 733641 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.05→91.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13162 0 113 1748 15023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01914178
X-RAY DIFFRACTIONr_bond_other_d0.0030.0213249
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.94719411
X-RAY DIFFRACTIONr_angle_other_deg1.135330593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19551853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37823.933661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.747152296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0561598
X-RAY DIFFRACTIONr_chiral_restr0.1340.22077
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02116329
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023347
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_it0.980.9736948
X-RAY DIFFRACTIONr_mcbond_other0.980.9736947
X-RAY DIFFRACTIONr_mcangle_it1.1931.4718730
X-RAY DIFFRACTIONr_mcangle_other1.1931.4718731
X-RAY DIFFRACTIONr_scbond_it2.21.2137230
X-RAY DIFFRACTIONr_scbond_other2.21.2127220
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4491.73710549
X-RAY DIFFRACTIONr_long_range_B_refined2.73213.2416986
X-RAY DIFFRACTIONr_long_range_B_other2.40912.61316558
X-RAY DIFFRACTIONr_rigid_bond_restr3.428327427
X-RAY DIFFRACTIONr_sphericity_free20.68251079
X-RAY DIFFRACTIONr_sphericity_bonded7.343527594
LS refinement shellResolution: 1.05→1.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 2843 -
Rwork0.246 53579 -
obs--99.03 %

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