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

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Basic information

Entry
Database: PDB / ID: 7qop
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: 1.8 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 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set
Revision 1.2Jan 31, 2024Group: Database references / Refinement description
Category: 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 1.3Nov 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)50,3425
Polymers50,2232
Non-polymers1193
Water6,143341
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)100,68410
Polymers100,4464
Non-polymers2376
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_777-y+2,-x+2,-z+5/21
Buried area22530 Å2
ΔGint-147 kcal/mol
Surface area32880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.499, 106.499, 83.006
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Nitrile hydratase


Mass: 23658.992 Da / Num. of mol.: 1 / Fragment: chain A / Mutation: I47S
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

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Non-polymers , 4 types, 344 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.: 1 / 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.: 341 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
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: 1.8→75.31 Å / Num. obs: 615278 / % possible obs: 100 % / Redundancy: 13.76 % / Biso Wilson estimate: 11.46 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 44724 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
d*TREKdata scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hht

3hht


Resolution: 1.8→75.31 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.469 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 2221 5 %RANDOM
Rwork0.178 ---
obs0.18 41933 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.85 Å2 / Biso mean: 17.52 Å2 / Biso min: 8.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 1.8→75.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 3 341 3831
Biso mean--19.5 26.85 -
Num. residues----429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223595
X-RAY DIFFRACTIONr_bond_other_d0.0010.022519
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.9664876
X-RAY DIFFRACTIONr_angle_other_deg1.04636101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.795431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29823.218174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9715614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1331529
X-RAY DIFFRACTIONr_chiral_restr0.1320.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02752
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 169 -
Rwork0.252 3065 -
all-3234 -
obs--99.42 %

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