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- PDB-5a4i: The mechanism of Hydrogen activation by NiFE-hydrogenases -

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Basic information

Entry
Database: PDB / ID: 5a4i
TitleThe mechanism of Hydrogen activation by NiFE-hydrogenases
Components(Hydrogenase-1 ...) x 2
KeywordsOXIDOREDUCTASE / HYDROGEN ACTIVATION / NIFE-HYDROGENASE / FES CLUSTER
Function / homology
Function and homology information


hydrogen metabolic process / fermentation / anaerobic electron transport chain / hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration ...hydrogen metabolic process / fermentation / anaerobic electron transport chain / hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / periplasmic side of plasma membrane / hydrogenase (acceptor) activity / 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
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 / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B ...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 / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / : / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / 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 / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / Hydrogenase-1 large chain / Hydrogenase-1 small chain
Similarity search - Component
Biological speciesESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsEvans, R.M. / Brooke, E.J. / Wehlin, S.A.M. / Nomerotskaia, E. / Sargent, F. / Carr, S.C. / Phillips, S.E.V. / Armstrong, F.A.
CitationJournal: Nat. Chem. Biol. / Year: 2016
Title: Mechanism of hydrogen activation by [NiFe] hydrogenases.
Authors: Evans, R.M. / Brooke, E.J. / Wehlin, S.A. / Nomerotskaia, E. / Sargent, F. / Carr, S.B. / Phillips, S.E. / Armstrong, F.A.
History
DepositionJun 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Oct 24, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / entity_src_nat / pdbx_struct_mod_residue / struct_ref / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.identifier_ORCID / _entity.pdbx_description / _entity.src_method / _entity_name_com.name / _pdbx_struct_mod_residue.details / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Hydrogenase-1 large chain
M: Hydrogenase-1 large chain
S: Hydrogenase-1 small chain
T: Hydrogenase-1 small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,88924
Polymers203,1624
Non-polymers3,72720
Water16,844935
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26230 Å2
ΔGint-327.7 kcal/mol
Surface area46640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.780, 97.580, 182.880
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 LMST

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


Mass: 64766.402 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 1-582 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria)
Gene: hyaB, b0973, JW0955
Production host: ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria)
References: UniProt: P0ACD8, hydrogenase (acceptor)
#2: Protein Hydrogenase-1 small chain / HYD1 / Membrane-bound hydrogenase 1 small subunit / NiFe hydrogenase


Mass: 36814.676 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 46-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria)
Gene: hyaA, b0972, JW0954
Production host: ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria)
References: UniProt: P69739, hydrogenase (acceptor)

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Sugars , 1 types, 2 molecules

#10: 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 , 9 types, 953 molecules

#3: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


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


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#9: Chemical ChemComp-SF3 / FE4-S3 CLUSTER


Mass: 319.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S3
#11: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 935 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsMUTATION D574N CREATED TO TEST FUNCTIONALITY

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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: 43.8 %
Description: MERGING R FOR HIGHEST RESOLUTION BIN 2.5, CCHALF 0.5
Crystal growpH: 6
Details: 100 MM BIS TRIS PH 5.9, 22% (W/V) PEG 3350, 200 MM LISO4, 150 MM NACL, 1 MM TCEP, 0.02 % DDM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97944
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 1.23→32.53 Å / Num. obs: 468877 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.2
Reflection shellResolution: 1.23→1.26 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.3 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3USC

3usc


Resolution: 1.23→32.19 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.291 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.14689 23652 5 %RANDOM
Rwork0.1239 ---
obs0.12507 445141 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.032 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.23→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13170 0 104 935 14209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01914093
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213164
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.94519260
X-RAY DIFFRACTIONr_angle_other_deg1.098330376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12351820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22523.891663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.003152285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.79915100
X-RAY DIFFRACTIONr_chiral_restr0.1150.22046
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02116200
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023338
X-RAY DIFFRACTIONr_nbd_refined0.2430.28322
X-RAY DIFFRACTIONr_nbd_other0.2250.224664
X-RAY DIFFRACTIONr_nbtor_refined0.1830.213886
X-RAY DIFFRACTIONr_nbtor_other0.0960.212866
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2476
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.080.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0861.1776907
X-RAY DIFFRACTIONr_mcbond_other1.0861.1776906
X-RAY DIFFRACTIONr_mcangle_it1.291.7778664
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7941.4597186
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8342.07510488
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.64127257
X-RAY DIFFRACTIONr_sphericity_free17.9335287
X-RAY DIFFRACTIONr_sphericity_bonded5.87827489
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 1690 -
Rwork0.319 31856 -
obs--94.78 %

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