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- PDB-6z8m: Structure of [NiFeSe] hydrogenase G491S variant from Desulfovibri... -

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Basic information

Entry
Database: PDB / ID: 6z8m
TitleStructure of [NiFeSe] hydrogenase G491S variant from Desulfovibrio vulgaris Hildenborough pressurized with Oxygen gas - structure G491S-O2
Components(Periplasmic [NiFeSe] hydrogenase, ...) x 2
KeywordsOXIDOREDUCTASE / Hydrogenase / Selenium / gas channels / high-pressure derivatization
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / cell envelope / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / cell envelope / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding / membrane
Similarity search - Function
: / : / [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 ...: / : / [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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
oxygen-damaged SF4 / CARBONMONOXIDE-(DICYANO) IRON / : / HYDROSULFURIC ACID / NICKEL (II) ION / OXYGEN MOLECULE / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase large subunit / cytochrome-c3 hydrogenase
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsZacarias, S. / Temporao, A. / Carpentier, P. / van der Linden, P. / Pereira, I.A.C. / Matias, P.M.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BBB-BEP/2885/2014 Portugal
Fundacao para a Ciencia e a TecnologiaLISBOA-01-0145-FEDER-007660 Portugal
CitationJournal: J.Biol.Inorg.Chem. / Year: 2020
Title: Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen.
Authors: Zacarias, S. / Temporao, A. / Carpentier, P. / van der Linden, P. / Pereira, I.A.C. / Matias, P.M.
History
DepositionJun 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic [NiFeSe] hydrogenase, small subunit
B: Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,77316
Polymers83,6752
Non-polymers2,09914
Water12,322684
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-137 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.993, 62.639, 110.532
Angle α, β, γ (deg.)90.000, 105.211, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Periplasmic [NiFeSe] hydrogenase, ... , 2 types, 2 molecules AB

#1: Protein Periplasmic [NiFeSe] hydrogenase, small subunit


Mass: 30261.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria)
Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Gene: hysB, DVU_1917
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72AS4, ferredoxin hydrogenase
#2: Protein Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing


Mass: 53413.086 Da / Num. of mol.: 1 / Mutation: G491S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria)
Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Gene: hysA, DVU_1918
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72AS3, ferredoxin hydrogenase

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Non-polymers , 10 types, 698 molecules

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


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-6ML / oxygen-damaged SF4


Mass: 383.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4O2S4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2O
#7: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#8: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#9: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#10: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.79 Å3/Da / Density % sol: 31.3 % / Description: thin plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 20% PEG 1500 (w/v) and 0.1 mM Tris-HCl pH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.02→53.33 Å / Num. obs: 331872 / % possible obs: 94.6 % / Redundancy: 2.7 % / Biso Wilson estimate: 8.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.04 / Net I/σ(I): 7.6
Reflection shellResolution: 1.02→1.04 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.098 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 16250 / CC1/2: 0.349 / Rpim(I) all: 0.781 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSK

5jsk


Resolution: 1.02→53.33 Å / SU ML: 0.1179 / Cross valid method: FREE R-VALUE / σ(F): 0.92 / Phase error: 16.3404
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: UNIQUE REFLECTIONS (NON-ANOMALOUS) USED IN REFINEMENT: 331545. Hydrogen atoms were included in calculated positions, solvent molecules were added manually in COOT using 2|Fo|-|Fc| and |Fo|- ...Details: UNIQUE REFLECTIONS (NON-ANOMALOUS) USED IN REFINEMENT: 331545. Hydrogen atoms were included in calculated positions, solvent molecules were added manually in COOT using 2|Fo|-|Fc| and |Fo|-|Fc| maps and occupancy factors were refined for disordered residues and the O2 molecules; anomalous dispersion parameters were refined for the selenium atom in Sec 489; anisotropic atomic displacement parameters were refined for all non-hydrogen and non-solvent atoms.
RfactorNum. reflection% reflectionSelection details
Rfree0.1509 30087 5 %Random selection
Rwork0.1342 571890 --
obs0.135 601977 86.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.78 Å2
Refinement stepCycle: LAST / Resolution: 1.02→53.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5877 0 67 684 6628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00686262
X-RAY DIFFRACTIONf_angle_d1.06448542
X-RAY DIFFRACTIONf_chiral_restr0.0806934
X-RAY DIFFRACTIONf_plane_restr0.00751106
X-RAY DIFFRACTIONf_dihedral_angle_d13.78362359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.030.34658740.338618394X-RAY DIFFRACTION83.85
1.03-1.050.33989590.321818724X-RAY DIFFRACTION84.64
1.05-1.060.32389560.307618682X-RAY DIFFRACTION84.87
1.06-1.070.30369540.298218480X-RAY DIFFRACTION84.48
1.07-1.090.28858900.283517749X-RAY DIFFRACTION80.78
1.09-1.10.27049610.261818991X-RAY DIFFRACTION86.19
1.1-1.120.2579960.244119267X-RAY DIFFRACTION87.31
1.12-1.130.2369160.22919161X-RAY DIFFRACTION87.37
1.13-1.150.233310330.220919135X-RAY DIFFRACTION87.65
1.15-1.170.23899300.211219278X-RAY DIFFRACTION87.07
1.17-1.190.216810220.206518996X-RAY DIFFRACTION86.64
1.19-1.210.215110780.199618782X-RAY DIFFRACTION85.95
1.21-1.240.21529410.196918113X-RAY DIFFRACTION82.48
1.24-1.260.200911010.179519189X-RAY DIFFRACTION87.83
1.26-1.290.180711120.166519525X-RAY DIFFRACTION89.35
1.29-1.320.18111130.156819449X-RAY DIFFRACTION89.33
1.32-1.350.158810140.145519706X-RAY DIFFRACTION89.53
1.35-1.390.148710620.140419642X-RAY DIFFRACTION89.53
1.39-1.430.151510270.130619646X-RAY DIFFRACTION89.39
1.43-1.480.1449390.123419168X-RAY DIFFRACTION87.02
1.48-1.530.13739870.115318731X-RAY DIFFRACTION85.32
1.53-1.590.12311030.099919964X-RAY DIFFRACTION91.29
1.59-1.660.11810720.095919953X-RAY DIFFRACTION90.89
1.66-1.750.120210930.094619737X-RAY DIFFRACTION90.1
1.75-1.860.12379710.098919526X-RAY DIFFRACTION88.79
1.86-20.11489960.099918935X-RAY DIFFRACTION86.25
2-2.20.109110320.096518510X-RAY DIFFRACTION84.65
2.2-2.520.11739770.096619332X-RAY DIFFRACTION87.94
2.52-3.180.12439930.110618964X-RAY DIFFRACTION86.33
3.18-53.330.13929850.12218161X-RAY DIFFRACTION82.82

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