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- PDB-6z8o: Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibri... -

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Basic information

Entry
Database: PDB / ID: 6z8o
TitleStructure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough pressurized with Krypton gas - structure G491A-Kr
Components(Periplasmic [NiFeSe] hydrogenase, ...) x 2
KeywordsOXIDOREDUCTASE / Hydrogenase / Selenium / gas channels / high-pressure derivatization
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / [Ni-Fe] 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 / metal ion binding / membrane
Similarity search - Function
: / : / [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 1. / Nickel-dependent hydrogenases large subunit signature 2. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site ...: / : / [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 1. / Nickel-dependent hydrogenases large subunit signature 2. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
oxygen-damaged SF4 / CARBONMONOXIDE-(DICYANO) IRON / : / HYDROSULFURIC ACID / KRYPTON / NICKEL (II) ION / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase large subunit / cytochrome-c3 hydrogenase
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZacarias, S. / Temporao, A. / Carpentier, P. / van der Linden, P. / Pereira, I.A.C. / Matias, P.M.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BBB-BEP/2885/2014 Portugal
Fundacao para a Ciencia e a TecnologiaLISBOA-01-0145-FEDER-007660 Portugal
CitationJournal: J.Biol.Inorg.Chem. / Year: 2020
Title: Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen.
Authors: Zacarias, S. / Temporao, A. / Carpentier, P. / van der Linden, P. / Pereira, I.A.C. / Matias, P.M.
History
DepositionJun 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Periplasmic [NiFeSe] hydrogenase, small subunit
D: Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,44642
Polymers167,2534
Non-polymers5,19338
Water68538
1
A: Periplasmic [NiFeSe] hydrogenase, small subunit
B: Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,30722
Polymers83,6272
Non-polymers2,68020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-151 kcal/mol
Surface area24010 Å2
MethodPISA
2
C: Periplasmic [NiFeSe] hydrogenase, small subunit
D: Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,13920
Polymers83,6272
Non-polymers2,51318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-141 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.716, 97.022, 121.318
Angle α, β, γ (deg.)90.000, 104.656, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 7 through 20 or resid 22 through 241 or resid 243 through 285))
d_2ens_1(chain "C" and (resid 7 through 20 or resid 22 through 241 or resid 243 through 285))
d_1ens_2(chain "B" and (resid 15 through 47 or resid 49...
d_2ens_2(chain "D" and (resid 15 through 47 or resid 49...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGGLYA1 - 14
d_12ens_1SERSERA17
d_13ens_1VALPROA20 - 238
d_14ens_1THRALAA242 - 282
d_15ens_1FS4FS4B
d_16ens_1FS4FS4C
d_21ens_1ARGGLYL2 - 15
d_22ens_1SERSERL18
d_23ens_1VALPROL21 - 239
d_24ens_1THRALAL243 - 283
d_25ens_1FS4FS4M
d_26ens_1FS4FS4N
d_11ens_2GLYLEUF1 - 33
d_12ens_2GLYASPF37 - 260
d_13ens_2PROTYRF264 - 374
d_14ens_2LEUPROF378 - 480
d_15ens_2LEULEUF484
d_16ens_2ALAHISF488 - 492
d_17ens_2FCOFCOG
d_18ens_2NINIH
d_19ens_2FE2FE2I
d_110ens_2H2SH2SJ
d_21ens_2GLYLEUQ1 - 33
d_22ens_2GLYASPQ37 - 260
d_23ens_2PROTYRQ264 - 374
d_24ens_2LEUPROQ378 - 480
d_25ens_2LEULEUQ484
d_26ens_2ALAHISQ488 - 492
d_27ens_2FCOFCOR
d_28ens_2NINIS
d_29ens_2FE2FE2T
d_210ens_2H2SH2SU

NCS ensembles :
ID
ens_1
ens_2

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Components

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Periplasmic [NiFeSe] hydrogenase, ... , 2 types, 4 molecules ACBD

#1: Protein Periplasmic [NiFeSe] hydrogenase, small subunit


Mass: 30261.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria)
Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / 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: 53365.086 Da / Num. of mol.: 2 / Mutation: G491A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria)
Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Gene: hysA, DVU_1918
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72AS3, ferredoxin hydrogenase

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Non-polymers , 9 types, 76 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Fe4S4
#4: Chemical ChemComp-6ML / oxygen-damaged SF4


Mass: 383.639 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4O2S4
#5: Chemical
ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Kr / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2O
#7: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#8: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#9: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.83 Å3/Da / Density % sol: 32.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.2→43.9 Å / Num. obs: 33895 / % possible obs: 49.1 % / Redundancy: 4 % / Biso Wilson estimate: 67.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.053 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.56 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1695 / CC1/2: 0.684 / Rpim(I) all: 0.404 / % possible all: 7.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSK

5jsk


Resolution: 2.2→39.12 Å / SU ML: 0.2872 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 38.3482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Hydrogen atoms were included in calculated positions, solvent molecules were added manually in COOT using 2|Fo|-|Fc| and |Fo|-|Fc| maps and occupancy factors were refined for disordered ...Details: Hydrogen atoms were included in calculated positions, solvent molecules were added manually in COOT using 2|Fo|-|Fc| and |Fo|-|Fc| maps and occupancy factors were refined for disordered residues and Kr atoms; isotropic atomic displacement parameters were refined. Non-crystallographic symmetry restraints were used and weight optimization was applied to lower the gap between the R-factor and the R-free.
RfactorNum. reflection% reflection
Rfree0.2747 1684 4.97 %
Rwork0.2258 32192 -
obs0.2282 33852 46.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11643 0 110 38 11791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004212119
X-RAY DIFFRACTIONf_angle_d0.930516490
X-RAY DIFFRACTIONf_chiral_restr0.04911795
X-RAY DIFFRACTIONf_plane_restr0.00542136
X-RAY DIFFRACTIONf_dihedral_angle_d15.92054510
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.36480263182
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.39526890243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.29140.403961X-RAY DIFFRACTION1.08
2.26-2.330.285760.3674173X-RAY DIFFRACTION3.02
2.33-2.420.3669170.3589390X-RAY DIFFRACTION6.79
2.42-2.510.4546320.3532665X-RAY DIFFRACTION11.52
2.51-2.630.3013440.3527906X-RAY DIFFRACTION15.68
2.63-2.770.3217760.34841335X-RAY DIFFRACTION23.12
2.77-2.940.38271160.32232169X-RAY DIFFRACTION37.96
2.94-3.170.33662150.30584411X-RAY DIFFRACTION76.17
3.17-3.490.30053120.27015611X-RAY DIFFRACTION97.48
3.49-3.990.29193060.2245533X-RAY DIFFRACTION95.55
3.99-5.020.23932720.1865103X-RAY DIFFRACTION88.07
5.02-39.120.23742840.18555835X-RAY DIFFRACTION98.65

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