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- PDB-7qou: A mutant of the nitrile hydratase from Geobacillus pallidus havin... -

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Basic information

Entry
Database: PDB / ID: 7qou
TitleA mutant of the nitrile hydratase from Geobacillus pallidus having enhanced thermostability
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, 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 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 / Electron transport accessory-like domain superfamily
Similarity search - Domain/homology
: / nitrile hydratase / Nitrile hydratase subunit beta
Similarity search - Component
Biological speciesAeribacillus pallidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsVan Wyk, J.C. / Cowan, D.A. / Danson, M.J. / Tsekoa, T.L. / Sayed, M.F. / Sewell, B.T.
Funding support South Africa, 1items
OrganizationGrant numberCountry
National Research Foundation in South Africa South Africa
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 1.2Oct 23, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,4056
Polymers51,2622
Non-polymers1434
Water7,044391
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)102,81112
Polymers102,5254
Non-polymers2868
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area22680 Å2
ΔGint-155 kcal/mol
Surface area32750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.084, 106.084, 82.975
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-561-

HOH

21B-466-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Nitrile hydratase


Mass: 24700.178 Da / Num. of mol.: 1 / Fragment: chain A / Mutation: M188V
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: 26562.209 Da / Num. of mol.: 1 / Fragment: chain B / Mutation: D96E, D167V
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

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Non-polymers , 4 types, 395 molecules

#3: Chemical ChemComp-CO / COBALT (II) ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.28 Å3/Da / Density % sol: 45.98 %
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→74.95 Å / Num. obs: 294741 / % possible obs: 98.5 % / Redundancy: 3.42 % / Rmerge(I) obs: 0.046 / Χ2: 0.96 / Net I/σ(I): 11
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 3.33 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3 / Num. unique obs: 86186 / Χ2: 1.42 / % possible all: 99.8

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Processing

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

2dpp


Resolution: 1.3→74.95 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.556 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1824 5740 5 %RANDOM
Rwork0.1527 ---
obs0.1542 108677 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.99 Å2 / Biso mean: 12.672 Å2 / Biso min: 7.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.3→74.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 4 391 3883
Biso mean--19.31 23.2 -
Num. residues----429
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 428 -
Rwork0.353 8008 -
all-8436 -
obs--99.32 %

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