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- PDB-7qov: The wild type nitrile hydratase from Geobacillus pallidus -

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Basic information

Entry
Database: PDB / ID: 7qov
TitleThe wild type nitrile hydratase from Geobacillus pallidus
Components
  • Nitrile hydratase
  • Nitrile hydratase subunit beta
KeywordsLYASE / heterotetramer
Function / homology
Function and homology information


indole-3-acetonitrile nitrile hydratase activity / nitrile hydratase / nitrile hydratase activity / transition metal ion binding
Similarity search - Function
Nitrile hydratase, beta subunit / Nitrile hydratase, alpha subunit / Nitrile hydratase, beta subunit / Nitrile hydratase beta subunit domain / Nitrile hydratase beta subunit, N-terminal / : / Nitrile hydratase beta subunit, C-terminal / Nitrile hydratase beta subunit, N-terminal / Nitrile hydratase alpha subunit /Thiocyanate hydrolase gamma subunit / Nitrile hydratase alpha /Thiocyanate hydrolase gamma ...Nitrile hydratase, beta subunit / Nitrile hydratase, alpha subunit / Nitrile hydratase, beta subunit / Nitrile hydratase beta subunit domain / Nitrile hydratase beta subunit, N-terminal / : / Nitrile hydratase beta subunit, C-terminal / Nitrile hydratase beta subunit, N-terminal / Nitrile hydratase alpha subunit /Thiocyanate hydrolase gamma subunit / Nitrile hydratase alpha /Thiocyanate hydrolase gamma / Nitrile hydratase, alpha chain / Nitrile hydratase alpha /Thiocyanate hydrolase gamma superfamily / SH3 type barrels. - #50 / Electron transport accessory-like domain superfamily / Cyclin A; domain 1 / SH3 type barrels. / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COBALT (III) ION / nitrile hydratase / Nitrile hydratase subunit beta
Similarity search - Component
Biological speciesAeribacillus pallidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVan Wyk, J.C. / Cowan, D.A. / Danson, M.J. / Tsekoa, T.L. / Sayed, M.F. / Sewell, B.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
National Research Foundation in South Africa United Kingdom
Royal Society United Kingdom
CitationJournal: Curr Res Struct Biol / Year: 2022
Title: Engineering enhanced thermostability into the Geobacillus pallidus nitrile hydratase.
Authors: Van Wyk, J.C. / Sewell, B.T. / Danson, M.J. / Tsekoa, T.L. / Sayed, M.F. / Cowan, D.A.
History
DepositionDec 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrile hydratase
B: Nitrile hydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4626
Polymers51,2962
Non-polymers1654
Water8,413467
1
A: Nitrile hydratase
B: Nitrile hydratase subunit beta
hetero molecules

A: Nitrile hydratase
B: Nitrile hydratase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,92312
Polymers102,5934
Non-polymers3318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_777-y+2,-x+2,-z+5/21
Buried area22020 Å2
ΔGint-185 kcal/mol
Surface area33970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.476, 105.476, 83.093
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-587-

HOH

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Components

#1: Protein Nitrile hydratase


Mass: 24732.242 Da / Num. of mol.: 1 / Fragment: chain A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeribacillus pallidus (bacteria) / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q84FS5, nitrile hydratase
#2: Protein Nitrile hydratase subunit beta / NHase


Mass: 26564.139 Da / Num. of mol.: 1 / Fragment: chain B
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeribacillus pallidus (bacteria) / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q84FS6, nitrile hydratase
#3: Chemical ChemComp-3CO / COBALT (III) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.4 % / Mosaicity: 0.72 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG400, 100mM magnesium chloride, 100mM MES (2[N-Morpholino]ethanesulfonic acid), 10-40mg/ml protein, pH 6.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.3→27.59 Å / Num. obs: 791949 / % possible obs: 88.5 % / Redundancy: 7.79 % / Rmerge(I) obs: 0.052 / Χ2: 0.95 / Net I/av σ(I): 14.6 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2% possible all
1.3-1.357.260.3314.41016311.3492.8
1.35-1.47.380.2815104821.2692.2
1.4-1.467.510.2276103891.1391.6
1.46-1.547.580.1757.4103551.0890.8
1.54-1.647.670.1310.4102540.9890
1.64-1.767.780.10111.5101720.8689.1
1.76-1.947.910.08214.9100910.888
1.94-2.228.090.07615.399390.7686.5
2.22-2.88.320.04623.998220.6784.4
2.8-27.598.530.02644.996080.6980

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Processing

Software
NameVersionClassification
d*TREK9.7Ldata scaling
PHENIX1.10.1refinement
PDB_EXTRACT3.27data extraction
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dpp

2dpp


Resolution: 1.4→27.59 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1799 --
obs-92064 99.9 %
Displacement parametersBiso max: 48.79 Å2 / Biso mean: 14.665 Å2 / Biso min: 6.28 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3489 0 4 467 3960

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