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- PDB-5jrd: E. coli Hydrogenase-1 variant P508A -

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Basic information

Entry
Database: PDB / ID: 5jrd
TitleE. coli Hydrogenase-1 variant P508A
Components(Hydrogenase-1 ...) x 2
KeywordsOXIDOREDUCTASE / Hydrogen activation / NiFe Hydrogenase
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 O6:H1 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsCarr, S.B. / Phillips, S.E.V. / Armstrong, F.A. / Evans, R.M. / Brooke, E.J. / Islam, S.T.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Biochemistry / Year: 2017
Title: Importance of the Active Site "Canopy" Residues in an O2-Tolerant [NiFe]-Hydrogenase.
Authors: Brooke, E.J. / Evans, R.M. / Islam, S.T. / Roberts, G.M. / Wehlin, S.A. / Carr, S.B. / Phillips, S.E. / Armstrong, F.A.
History
DepositionMay 6, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 10, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 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-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)205,91423
Polymers203,1124
Non-polymers2,80219
Water24,6991371
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24790 Å2
ΔGint-314 kcal/mol
Surface area48500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.691, 98.589, 185.373
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
Details: substrain MC4100
Source: (gene. exp.) Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria)
Gene: hyaA, c1113 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P69740, hydrogenase (acceptor)
#2: Protein Hydrogenase-1 large chain / HYD1 / Membrane-bound hydrogenase 1 large subunit / NiFe hydrogenase


Mass: 64741.348 Da / Num. of mol.: 2 / Mutation: P508A
Source method: isolated from a genetically manipulated source
Details: substrain MC4100
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hyaB, b0973, JW0955 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ACD8, hydrogenase (acceptor)

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Non-polymers , 9 types, 1390 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Fe4S4 / Details: substrain MC4100 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hyaA / Production host: Escherichia coli K-12 (bacteria)
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Fe3S4 / Details: substrain MC4100 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hyaA / Production host: Escherichia coli K-12 (bacteria)
#5: Chemical ChemComp-SF3 / FE4-S3 CLUSTER


Mass: 319.575 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Fe4S3 / Details: substrain MC4100 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hyaA / Production host: Escherichia coli K-12 (bacteria)
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Cl / Details: substrain MC4100 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hyaA / Production host: Escherichia coli K-12 (bacteria)
#7: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Mutation: P508A
Source method: isolated from a genetically manipulated source
Formula: C3FeN2O / Details: substrain MC4100 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hyaB / Production host: Escherichia coli K-12 (bacteria)
#8: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Mutation: P508A
Source method: isolated from a genetically manipulated source
Formula: Ni / Details: substrain MC4100 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hyaB / Production host: Escherichia coli K-12 (bacteria)
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Mutation: P508A
Source method: isolated from a genetically manipulated source
Formula: Mg / Details: substrain MC4100 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hyaB / Production host: Escherichia coli K-12 (bacteria)
#10: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Mutation: P508A
Source method: isolated from a genetically manipulated source
Formula: SO4 / Details: substrain MC4100 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hyaB / Production host: Escherichia coli K-12 (bacteria)
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1371 / 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: 2.28 Å3/Da / Density % sol: 46.1 % / Description: Rectangular rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Peg 3350, 50 mM Bis-tris, 200 mM LiSO4, 150 mM NaCl
PH range: 5.7-6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.2→98.6 Å / Num. obs: 536585 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.3
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb 5a4m

5a4m


Resolution: 1.2→92.69 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.169 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.029 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14052 26714 5 %RANDOM
Rwork0.12071 ---
obs0.12171 509698 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.32 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.2→92.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13242 0 5 1371 14618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01914127
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213213
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.94519347
X-RAY DIFFRACTIONr_angle_other_deg1.22330505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13251851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26223.906658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.099152305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5631598
X-RAY DIFFRACTIONr_chiral_restr0.1150.22077
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02116259
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023337
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_it1.1391.3476931
X-RAY DIFFRACTIONr_mcbond_other1.141.3476930
X-RAY DIFFRACTIONr_mcangle_it1.4112.0328699
X-RAY DIFFRACTIONr_mcangle_other1.4112.0318700
X-RAY DIFFRACTIONr_scbond_it2.0261.6067196
X-RAY DIFFRACTIONr_scbond_other1.9961.67182
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2562.31210505
X-RAY DIFFRACTIONr_long_range_B_refined2.85312.28116757
X-RAY DIFFRACTIONr_long_range_B_other2.55811.72816076
X-RAY DIFFRACTIONr_rigid_bond_restr5.823327340
X-RAY DIFFRACTIONr_sphericity_free23.1845385
X-RAY DIFFRACTIONr_sphericity_bonded7.659527896
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 1959 -
Rwork0.225 37362 -
obs--99.67 %

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