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- PDB-5jsu: The 3D structure of the U489C variant of [NiFeSe] hydrogenase fro... -

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Entry
Database: PDB / ID: 5jsu
TitleThe 3D structure of the U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough in the oxidized state at 1.40 Angstrom resolution
Components(Periplasmic [NiFeSe] hydrogenase, ...) x 2
KeywordsOXIDOREDUCTASE / NIFESE-SITE H2 CLEAVAGE/PRODUCTION
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 / Resolution: 1.4 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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_alt_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_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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)91,64011
Polymers89,8832
Non-polymers1,7579
Water12,809711
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-131 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.204, 62.655, 109.841
Angle α, β, γ (deg.)90.00, 104.97, 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: 55942.148 Da / Num. of mol.: 1 / Mutation: U489C
Source method: isolated from a genetically manipulated source
Details: Cys489 oxidized to sulfinate (CSD) in crystal structure
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, 720 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-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2O
#6: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / 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: 1.96 Å3/Da / Density % sol: 37.38 % / Description: irregular hexagonal plate
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / 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
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9701 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9701 Å / Relative weight: 1
ReflectionResolution: 1.4→45.4 Å / Num. obs: 136125 / % possible obs: 99.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 11.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2 / % possible all: 88.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZE9

3ze9


Resolution: 1.4→45.362 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 12.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1414 6833 5.02 %
Rwork0.1104 --
obs0.112 136118 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→45.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5871 0 45 711 6627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096366
X-RAY DIFFRACTIONf_angle_d1.1868656
X-RAY DIFFRACTIONf_dihedral_angle_d16.3042386
X-RAY DIFFRACTIONf_chiral_restr0.081937
X-RAY DIFFRACTIONf_plane_restr0.0071134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4004-1.41630.25962220.21513673X-RAY DIFFRACTION87
1.4163-1.4330.23052250.18544326X-RAY DIFFRACTION100
1.433-1.45050.22452240.17374278X-RAY DIFFRACTION100
1.4505-1.46880.20762070.16254353X-RAY DIFFRACTION100
1.4688-1.48820.20772510.15274256X-RAY DIFFRACTION100
1.4882-1.50860.16431930.13954342X-RAY DIFFRACTION100
1.5086-1.53010.17512530.12834328X-RAY DIFFRACTION100
1.5301-1.5530.16372430.12174232X-RAY DIFFRACTION100
1.553-1.57720.16572170.11584360X-RAY DIFFRACTION100
1.5772-1.60310.1512170.10984331X-RAY DIFFRACTION100
1.6031-1.63070.1492470.10174271X-RAY DIFFRACTION100
1.6307-1.66040.12752550.0964332X-RAY DIFFRACTION100
1.6604-1.69230.15942280.09844316X-RAY DIFFRACTION100
1.6923-1.72690.1412400.0964272X-RAY DIFFRACTION100
1.7269-1.76440.13222210.09264334X-RAY DIFFRACTION100
1.7644-1.80550.12772320.08914336X-RAY DIFFRACTION100
1.8055-1.85060.12022280.09094292X-RAY DIFFRACTION100
1.8506-1.90060.13472030.09224364X-RAY DIFFRACTION100
1.9006-1.95660.13012260.09184334X-RAY DIFFRACTION100
1.9566-2.01970.1252160.0934340X-RAY DIFFRACTION100
2.0197-2.09190.11832350.09354302X-RAY DIFFRACTION100
2.0919-2.17570.13012340.09594345X-RAY DIFFRACTION100
2.1757-2.27470.12812430.09744316X-RAY DIFFRACTION100
2.2747-2.39460.12892160.09514353X-RAY DIFFRACTION100
2.3946-2.54460.12772410.09614308X-RAY DIFFRACTION100
2.5446-2.74110.13122420.10224342X-RAY DIFFRACTION100
2.7411-3.01690.1372030.11264388X-RAY DIFFRACTION100
3.0169-3.45330.12422160.11654401X-RAY DIFFRACTION100
3.4533-4.35020.12942410.10784380X-RAY DIFFRACTION100
4.3502-45.38550.15122140.13394480X-RAY DIFFRACTION100

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