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- PDB-5jt1: The 3D structure of Ni-reconstituted U489C variant of [NiFeSe] hy... -

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Basic information

Entry
Database: PDB / ID: 5jt1
TitleThe 3D structure of Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough in the oxidized state at 1.35 Angstrom resolution
Components(Periplasmic [NiFeSe] hydrogenase, ...) x 2
KeywordsOXIDOREDUCTASE / NIFESE-SITE H2 CLEAVAGE/PRODUCTION
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / ferredoxin hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / metal ion binding
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
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 / Resolution: 1.35 Å
AuthorsMarques, M.C. / Pereira, I.A.C. / Matias, P.M.
Funding support Portugal, 3items
OrganizationGrant numberCountry
FUNDACAO PARA A CIENCIA E TECNOLOGIAPTDC/BBB-BEP/0934/2012 Portugal
FUNDACAO PARA A CIENCIA E TECNOLOGIAPEst OE/EQB/LA0004/2011 Portugal
FUNDACAO PARA A CIENCIA E TECNOLOGIASFRH/BD/60879/2009 Portugal
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: The direct role of selenocysteine in [NiFeSe] hydrogenase maturation and catalysis.
Authors: Marques, M.C. / Tapia, C. / Gutierrez-Sanz, O. / Ramos, A.R. / Keller, K.L. / Wall, J.D. / De Lacey, A.L. / Matias, P.M. / Pereira, I.A.C.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jan 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 / pdbx_struct_conn_angle / 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 / _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 1.3Apr 3, 2024Group: Derived calculations / Category: struct_conn
Item: _struct_conn.conn_type_id / _struct_conn.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_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
A: Periplasmic [NiFeSe] hydrogenase, small subunit
B: Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,59010
Polymers89,8672
Non-polymers1,7238
Water13,655758
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-122 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.778, 63.183, 110.664
Angle α, β, γ (deg.)90.00, 105.27, 90.00
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: 33940.879 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
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72AS4, ferredoxin hydrogenase
#2: Protein Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing


Mass: 55926.148 Da / Num. of mol.: 1 / Mutation: U489C
Source method: isolated from a genetically manipulated source
Details: Cys489 is oxidized to sulfinate (CSD)
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: hysA, DVU_1918
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72AS3, ferredoxin hydrogenase

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Non-polymers , 7 types, 766 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / 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-FCO / CARBONMONOXIDE-(DICYANO) IRON


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


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


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


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 758 / 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 Å3/Da / Density % sol: 38.62 % / Description: irregular hexagonal plate
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350 and 0.2M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.35→45.6 Å / Num. obs: 151830 / % possible obs: 97.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 10
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.177 / Mean I/σ(I) obs: 1.3 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSMarch 1, 2015data reduction
XDSMarch 1, 2015data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WPN

2wpn


Resolution: 1.35→45.626 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 14.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.145 7574 4.99 %Random selection
Rwork0.1159 ---
obs0.1174 151825 97.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→45.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 44 758 6684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126361
X-RAY DIFFRACTIONf_angle_d1.2278655
X-RAY DIFFRACTIONf_dihedral_angle_d14.8592398
X-RAY DIFFRACTIONf_chiral_restr0.085946
X-RAY DIFFRACTIONf_plane_restr0.0081128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.26052350.23254686X-RAY DIFFRACTION96
1.3653-1.38140.28682580.23374689X-RAY DIFFRACTION96
1.3814-1.39830.28652320.22594733X-RAY DIFFRACTION96
1.3983-1.4160.26382220.20994765X-RAY DIFFRACTION96
1.416-1.43460.25772470.20294730X-RAY DIFFRACTION96
1.4346-1.45420.2312290.18664695X-RAY DIFFRACTION96
1.4542-1.4750.20822650.17194794X-RAY DIFFRACTION97
1.475-1.4970.19322390.16324702X-RAY DIFFRACTION97
1.497-1.52040.19712300.15464779X-RAY DIFFRACTION97
1.5204-1.54540.19432560.14814756X-RAY DIFFRACTION97
1.5454-1.5720.19262710.14184748X-RAY DIFFRACTION97
1.572-1.60060.1672270.1284798X-RAY DIFFRACTION97
1.6006-1.63140.17142550.1194801X-RAY DIFFRACTION97
1.6314-1.66470.14562410.11684765X-RAY DIFFRACTION97
1.6647-1.70090.1622380.11694828X-RAY DIFFRACTION97
1.7009-1.74040.15522760.10954723X-RAY DIFFRACTION97
1.7404-1.7840.1292580.09974833X-RAY DIFFRACTION98
1.784-1.83220.1462590.10014789X-RAY DIFFRACTION98
1.8322-1.88610.13892710.0984785X-RAY DIFFRACTION98
1.8861-1.9470.13162540.09864844X-RAY DIFFRACTION98
1.947-2.01660.14382780.09614820X-RAY DIFFRACTION98
2.0166-2.09730.12792810.09384826X-RAY DIFFRACTION98
2.0973-2.19280.12012790.09124849X-RAY DIFFRACTION98
2.1928-2.30840.11182400.09024871X-RAY DIFFRACTION99
2.3084-2.4530.11392500.09274878X-RAY DIFFRACTION99
2.453-2.64240.12312380.10044924X-RAY DIFFRACTION99
2.6424-2.90830.13412650.10594880X-RAY DIFFRACTION99
2.9083-3.3290.13152750.11514928X-RAY DIFFRACTION99
3.329-4.19370.12972080.10545024X-RAY DIFFRACTION99
4.1937-45.6520.132970.12145008X-RAY DIFFRACTION99

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