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- PDB-5jsh: The 3D structure of recombinant [NiFeSe] hydrogenase from Desulfo... -

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Basic information

Entry
Database: PDB / ID: 5jsh
TitleThe 3D structure of recombinant [NiFeSe] hydrogenase from Desulfovibrio Vulgaris Hildenborough in the oxidized state at 1.30 Angstrom
Components(Periplasmic [NiFeSe] hydrogenase, ...) x 2
KeywordsOXIDOREDUCTASE / hydrogenase / biological hydrogen production
Function / homology
Function and homology information


ferredoxin hydrogenase / cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding ...ferredoxin hydrogenase / cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / 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 ...: / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 TecnologiaSFRH/BD/60879/2009 Portugal
Fundacao para a Ciencia e TecnologiaPEst OE/EQB/LA0004/2011 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 8, 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

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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)91,68811
Polymers89,9302
Non-polymers1,7599
Water15,421856
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-133 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.220, 63.460, 111.080
Angle α, β, γ (deg.)90.00, 105.15, 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 (strain Hildenborough / ATCC 29579 / NCIMB 8303) (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: 55989.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cysteine 75 is oxidized to sulfenate (CSD) in the crystal structure
Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303) (bacteria)
Gene: hysA, DVU_1918
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72AS3, ferredoxin hydrogenase

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Non-polymers , 8 types, 865 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-NI / NICKEL (II) ION


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


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 856 / 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: 2.07 Å3/Da / Density % sol: 40.59 % / Description: irregular hexagonal plate
Crystal growTemperature: 295 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: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.3→54 Å / Num. obs: 169426 / % possible obs: 96.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.7
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.2 / % possible all: 70.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WPN

2wpn


Resolution: 1.3→51.819 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 0.68 / Phase error: 13.22 / Stereochemistry target values: ML
Details: THE ANOMALOUS DISPERSION PARAMETERS FOR THE SE ATOM WERE REFINED. HYDROGEN ATOMS WERE ADDED IN CALCULATED POSITIONS AND REFINED IN RIDING POSITIONS. INDIVIDUAL ANISOTROPIC ATOMIC ...Details: THE ANOMALOUS DISPERSION PARAMETERS FOR THE SE ATOM WERE REFINED. HYDROGEN ATOMS WERE ADDED IN CALCULATED POSITIONS AND REFINED IN RIDING POSITIONS. INDIVIDUAL ANISOTROPIC ATOMIC DISPLACEMENT PARAMETERS FOR ALL PROTEIN NON- HYDROGEN ATOMS WERE REFINED.
RfactorNum. reflection% reflection
Rfree0.1354 14892 5.01 %
Rwork0.1131 --
obs0.1142 169417 86.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→51.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5869 0 45 856 6770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096349
X-RAY DIFFRACTIONf_angle_d1.0688649
X-RAY DIFFRACTIONf_dihedral_angle_d14.1332404
X-RAY DIFFRACTIONf_chiral_restr0.082940
X-RAY DIFFRACTIONf_plane_restr0.0071132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.24243070.22755860X-RAY DIFFRACTION54
1.3148-1.33030.23233680.21947023X-RAY DIFFRACTION65
1.3303-1.34650.24154080.20257683X-RAY DIFFRACTION69
1.3465-1.36350.21484380.19338309X-RAY DIFFRACTION78
1.3635-1.38150.21425300.17989140X-RAY DIFFRACTION84
1.3815-1.40040.19184770.17039339X-RAY DIFFRACTION86
1.4004-1.42040.20484720.15649336X-RAY DIFFRACTION86
1.4204-1.44160.18635180.14489388X-RAY DIFFRACTION85
1.4416-1.46410.17995400.13519263X-RAY DIFFRACTION86
1.4641-1.48810.17055150.13139327X-RAY DIFFRACTION86
1.4881-1.51380.15774680.12429453X-RAY DIFFRACTION86
1.5138-1.54130.14754760.11689459X-RAY DIFFRACTION86
1.5413-1.5710.13594310.11239329X-RAY DIFFRACTION86
1.571-1.6030.13994780.10489397X-RAY DIFFRACTION86
1.603-1.63790.13515110.09929464X-RAY DIFFRACTION86
1.6379-1.6760.11985210.09819325X-RAY DIFFRACTION86
1.676-1.71790.13185120.09759410X-RAY DIFFRACTION86
1.7179-1.76440.12775260.09699360X-RAY DIFFRACTION86
1.7644-1.81630.13945230.09599377X-RAY DIFFRACTION86
1.8163-1.87490.11744830.10199339X-RAY DIFFRACTION86
1.8749-1.94190.12974650.10599261X-RAY DIFFRACTION85
1.9419-2.01970.12394800.1059314X-RAY DIFFRACTION85
2.0197-2.11160.12684440.10259356X-RAY DIFFRACTION85
2.1116-2.22290.12575660.104210850X-RAY DIFFRACTION100
2.2229-2.36220.11675830.102810933X-RAY DIFFRACTION100
2.3622-2.54460.11555830.098410881X-RAY DIFFRACTION100
2.5446-2.80070.1275280.102910826X-RAY DIFFRACTION99
2.8007-3.20590.13085600.113210799X-RAY DIFFRACTION99
3.2059-4.03880.12935820.110710636X-RAY DIFFRACTION98
4.0388-51.85970.12535990.114410721X-RAY DIFFRACTION98

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