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- PDB-6ruc: THE 3D STRUCTURE OF [NIFESE] HYDROGENASE G491S VARIANT FROM DESUL... -

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Basic information

Entry
Database: PDB / ID: 6ruc
TitleTHE 3D STRUCTURE OF [NIFESE] HYDROGENASE G491S VARIANT FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 1.20 ANGSTROM RESOLUTION
Components(Periplasmic [NiFeSe] hydrogenase, ...) x 2
KeywordsOXIDOREDUCTASE / NIFESE-SITE / H2 CLEAVAGE/PRODUCTION / O2 TOLERANCE
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / cell envelope / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / cell envelope / anaerobic respiration / 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
: / 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 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
oxygen-damaged SF4 / CARBONMONOXIDE-(DICYANO) IRON / : / HYDROSULFURIC ACID / NICKEL (II) ION / IRON/SULFUR CLUSTER / Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing / cytochrome-c3 hydrogenase
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.199 Å
AuthorsMatias, P.M. / Zacarias, S. / Pereita, I.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BBB-BEP/2885/2014 Portugal
Fundacao para a Ciencia e a TecnologiaSFRH/BD/100314/2014 Portugal
CitationJournal: Acs Catalysis / Year: 2019
Title: A Hydrophilic Channel Is Involved in Oxidative Inactivation of a [NiFeSe] Hydrogenase
Authors: Zacarias, S. / Temporao, A. / del Barrio, M. / Fourmond, V. / Leger, C. / Matias, P.M. / Pereira, I.A.C.
History
DepositionMay 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / refine / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _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

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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)86,66013
Polymers84,7172
Non-polymers1,94311
Water11,728651
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-142 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.410, 63.589, 110.705
Angle α, β, γ (deg.)90.000, 104.880, 90.000
Int Tables number5
Space group name H-MC121

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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 str. Hildenborough (bacteria)
Gene: hysB, DVU_1917 / Variant: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72AS4, ferredoxin hydrogenase
#2: Protein Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing


Mass: 54455.223 Da / Num. of mol.: 1 / Mutation: G491S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: hysA, DVU_1918 / Variant: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72AS3, ferredoxin hydrogenase

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Non-polymers , 9 types, 662 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.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 1500 (w/v), 0.1 M Tris-HCl pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.2→45.73 Å / Num. obs: 216144 / % possible obs: 97.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.042 / Rrim(I) all: 0.11 / Net I/σ(I): 9.4 / Num. measured all: 1414791
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.2-1.225.61.3255021390230.5090.61.461.283
6.57-45.736.50.038923314270.9980.0160.04239.299.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.8 Å45.73 Å
Translation1.8 Å45.73 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimless0.5.28data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSH

5jsh


Resolution: 1.199→45.733 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.11 / Phase error: 16.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1484 21204 4.99 %
Rwork0.1276 403816 -
obs0.1286 425020 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.09 Å2 / Biso mean: 16.2158 Å2 / Biso min: 8 Å2
Refinement stepCycle: final / Resolution: 1.199→45.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5870 0 77 671 6618
Biso mean--23.33 27.73 -
Num. residues----766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1988-1.21250.2975460.286103631090975
1.2125-1.22670.32286330.2822131281376195
1.2267-1.24170.28887200.2659134611418198
1.2417-1.25740.27656790.2586136911437098
1.2574-1.2740.2587170.2495134851420299
1.274-1.29140.25896550.2395136481430398
1.2914-1.30990.26257100.2372136991440999
1.3099-1.32940.23717920.2272135241431699
1.3294-1.35020.25096600.2229136131427399
1.3502-1.37230.24187290.2134136461437599
1.3723-1.3960.23116320.2003137291436199
1.396-1.42140.21216620.1839136361429898
1.4214-1.44870.19957610.1738135411430298
1.4487-1.47830.19057620.1715134331419598
1.4783-1.51040.18877740.1556131341390895
1.5104-1.54560.15277520.1354136221437499
1.5456-1.58420.1536950.1293137131440899
1.5842-1.62710.14496750.1144137681444399
1.6271-1.6750.13317320.1062136181435099
1.675-1.7290.12837210.0997136521437399
1.729-1.79080.12227330.097136191435299
1.7908-1.86250.12027550.0933136931444899
1.8625-1.94730.1147320.0916136061433899
1.9473-2.050.1117700.0902133581412897
2.05-2.17840.11477300.0903132691399997
2.1784-2.34660.11397650.0915137021446799
2.3466-2.58270.11456950.0908136931438899
2.5827-2.95640.11796830.0977136551433899
2.9564-3.72440.12226450.1073136151426098
3.7244-45.76660.14216890.1297135021419198

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