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- PDB-5mdl: Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralst... -

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Entry
Database: PDB / ID: 5mdl
TitleCrystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its O2-derivatized form by a "soak-and-freeze" derivatization method
Components(Uptake hydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / [NIFE] HYDROGENASE / KNALLGASBACTERIA / PROTEOBACTERIA / AEROBIC HYDROGEN BACTERIA / OXYGEN DERIVATISATION / DEHYDROGENASE / HYDROGEN CATALYSIS / METALLOENZYME / DIHYDROGEN / BIMETALLIC / METALLOPROTEIN CATALYTIC CENTER / NI-FE ACTIVE SITE / T-CLUSTER / FE-S CLUSTER / [4Fe-3S] CLUSTER / [3Fe-4S] CLUSTER / [4Fe-4S] CLUSTER / OXYGEN DERIVATISED STATE / OXIDIZED STATE / OXYGEN TOLERANT HYDROGENASE / MEMBRANE BOUND / MEMBRANE / HYDROPHOBIC TUNNEL / GAS TRANSPORT
Function / homology
Function and homology information


hydrogenase (acceptor) / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / 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 / FE4-S3 CLUSTER / NI-FE OXIDIZED ACTIVE CENTER / OXYGEN ATOM / OXYGEN MOLECULE / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / Uptake hydrogenase large subunit / Uptake hydrogenase small subunit
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsKalms, J. / Schmidt, A. / Scheerer, P.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationCluster of Excellence - Unifying Concepts in Catalysis - UniCat - (EXC 314) Germany
German Research FoundationSFB 740-B6 Germany
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase.
Authors: Kalms, J. / Schmidt, A. / Frielingsdorf, S. / Utesch, T. / Gotthard, G. / von Stetten, D. / van der Linden, P. / Royant, A. / Mroginski, M.A. / Carpentier, P. / Lenz, O. / Scheerer, P.
History
DepositionNov 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 2.0Mar 28, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle
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 / _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 3.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle
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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 3.1Jan 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_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.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.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Uptake hydrogenase large subunit;HOXG
S: Uptake hydrogenase small subunit;HOXK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,76214
Polymers103,2742
Non-polymers1,48712
Water10,863603
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-93 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.134, 95.568, 119.686
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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Uptake hydrogenase ... , 2 types, 2 molecules LS

#1: Protein Uptake hydrogenase large subunit;HOXG / Hydrogenlyase / Membrane-bound hydrogenase large subunit


Mass: 67247.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Production host: Ralstonia eutropha H16 (bacteria) / Strain (production host): H16 DSM 428 STANIER 337 / References: UniProt: P31891, hydrogenase (acceptor)
#2: Protein Uptake hydrogenase small subunit;HOXK / Hydrogenlyase / Membrane-bound hydrogenase small subunit


Mass: 36027.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Production host: Ralstonia eutropha H16 (bacteria) / Strain (production host): H16 DSM 428 STANIER 337 / References: UniProt: P31892, hydrogenase (acceptor)

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Non-polymers , 10 types, 615 molecules

#3: Chemical ChemComp-NFV / NI-FE OXIDIZED ACTIVE CENTER


Mass: 210.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2NiO2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#9: Chemical ChemComp-F4S / FE4-S3 CLUSTER / T-CLUSTER


Mass: 319.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S3
#10: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.02 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 20-30% PEG3350, 0.1M BIS-TRIS pH 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2016 / Details: Mirror
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.41→47.78 Å / Num. obs: 155314 / % possible obs: 96.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 10.7
Reflection shellResolution: 1.41→1.49 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 2 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RGW

3rgw


Resolution: 1.41→47.78 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.414 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1632 7817 5 %RANDOM
Rwork0.13153 ---
obs0.13312 147390 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.599 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å2-0 Å2
2---0.57 Å20 Å2
3---0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.41→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6765 0 49 603 7417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0387114
X-RAY DIFFRACTIONr_bond_other_d0.0050.0226647
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9599704
X-RAY DIFFRACTIONr_angle_other_deg0.8323.00115321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5223.781320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.629151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3741545
X-RAY DIFFRACTIONr_chiral_restr0.0760.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218170
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021667
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_it1.3411.8383528
X-RAY DIFFRACTIONr_mcbond_other1.3391.8373527
X-RAY DIFFRACTIONr_mcangle_it1.5962.7634420
X-RAY DIFFRACTIONr_mcangle_other1.5962.7644421
X-RAY DIFFRACTIONr_scbond_it1.4482.013586
X-RAY DIFFRACTIONr_scbond_other1.4482.013586
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6812.9465264
X-RAY DIFFRACTIONr_long_range_B_refined2.43915.7528822
X-RAY DIFFRACTIONr_long_range_B_other2.43815.7548823
X-RAY DIFFRACTIONr_rigid_bond_restr2.035313761
X-RAY DIFFRACTIONr_sphericity_free20.9295183
X-RAY DIFFRACTIONr_sphericity_bonded5.788514015
LS refinement shellResolution: 1.41→1.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 555 -
Rwork0.255 10483 -
obs--93.29 %

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