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- PDB-6rtp: THE 3D STRUCTURE OF [NIFESE] HYDROGENASE G50T VaRIANT FROM DESULF... -

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Basic information

Entry
Database: PDB / ID: 6rtp
TitleTHE 3D STRUCTURE OF [NIFESE] HYDROGENASE G50T VaRIANT FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 1.10 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 / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 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 24, 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

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)86,76614
Polymers84,7312
Non-polymers2,03512
Water14,394799
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-134 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.138, 62.712, 110.240
Angle α, β, γ (deg.)90.000, 105.107, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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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)
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: 54469.246 Da / Num. of mol.: 1 / Mutation: G50T
Source method: isolated from a genetically manipulated source
Details: Cys 75 partially oxidized to sulfenate/sulfinate
Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / 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 , 9 types, 811 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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 / Nickel


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 / Hydrogen sulfide


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


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


Mass: 18.015 Da / Num. of mol.: 799 / 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: 41.93 % / Description: Plate
Crystal growTemperature: 295 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: ID29 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.1→45.38 Å / Num. obs: 263501 / % possible obs: 93.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 11.03 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.061 / Rrim(I) all: 0.098 / Net I/σ(I): 6.1 / Num. measured all: 617436
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
1.1-1.122.30.99527637119720.3280.7851.272185.7
6.02-45.382.40.053414217150.9890.0430.06919.494.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.74 Å45.38 Å
Translation6.74 Å45.38 Å

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimless0.5.27data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSH

5jsh


Resolution: 1.1→45.38 Å / SU ML: 0.1206 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 18.2096
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1578 22626 5.08 %
Rwork0.1393 422771 -
obs0.1402 445397 79.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.24 Å2
Refinement stepCycle: LAST / Resolution: 1.1→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5876 0 63 799 6738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00766352
X-RAY DIFFRACTIONf_angle_d1.33668698
X-RAY DIFFRACTIONf_chiral_restr0.0892947
X-RAY DIFFRACTIONf_plane_restr0.00761129
X-RAY DIFFRACTIONf_dihedral_angle_d13.9512428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.3296080.317912413X-RAY DIFFRACTION69.98
1.11-1.120.31746410.306313232X-RAY DIFFRACTION74.18
1.12-1.140.31497000.304413031X-RAY DIFFRACTION73.86
1.14-1.150.31787200.294812861X-RAY DIFFRACTION73.35
1.15-1.170.30817090.286711990X-RAY DIFFRACTION68.15
1.17-1.180.29047950.286813610X-RAY DIFFRACTION76.87
1.18-1.20.29267390.274713686X-RAY DIFFRACTION78.01
1.2-1.220.28247520.265713817X-RAY DIFFRACTION78.15
1.22-1.240.27797270.256813838X-RAY DIFFRACTION78.46
1.24-1.260.24947390.245313887X-RAY DIFFRACTION78.03
1.26-1.280.25457220.231813865X-RAY DIFFRACTION78.38
1.28-1.30.23777170.223813742X-RAY DIFFRACTION78
1.3-1.330.23757490.214913534X-RAY DIFFRACTION76.85
1.33-1.360.24077070.20212746X-RAY DIFFRACTION72.25
1.36-1.390.1997420.18314328X-RAY DIFFRACTION80.9
1.39-1.420.18038310.163914362X-RAY DIFFRACTION81.7
1.42-1.450.17077440.155314592X-RAY DIFFRACTION82.09
1.45-1.490.17167210.141214560X-RAY DIFFRACTION82.09
1.49-1.540.1628450.12714486X-RAY DIFFRACTION82.35
1.54-1.590.14047540.119514500X-RAY DIFFRACTION82.04
1.59-1.640.1347730.109114025X-RAY DIFFRACTION79.59
1.64-1.710.12387360.102713674X-RAY DIFFRACTION77.33
1.71-1.790.12038550.09815249X-RAY DIFFRACTION86.65
1.79-1.880.12077910.100515323X-RAY DIFFRACTION86.5
1.88-20.11567770.101515265X-RAY DIFFRACTION86.03
2-2.150.11787340.098915201X-RAY DIFFRACTION85.69
2.15-2.370.11797190.103414155X-RAY DIFFRACTION79.98
2.37-2.710.1289280.10515475X-RAY DIFFRACTION88.13
2.71-3.420.13268290.115615828X-RAY DIFFRACTION89.51
3.42-45.420.14128220.128715496X-RAY DIFFRACTION87.59

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