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- PDB-7z0v: A mutant of the nitrile hydratase from Geobacillus pallidus havin... -

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Basic information

Entry
Database: PDB / ID: 7z0v
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


nitrile hydratase / indole-3-acetonitrile 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: 1.45 Å
AuthorsVan Wyk, J.C. / Cowan, D.A. / Danson, M.J. / Tsekoa, T.L. / Sayed, M.F. / Sewell, B.T.
Funding support South Africa, United Kingdom, 2items
OrganizationGrant numberCountry
National Research Foundation in South Africa South Africa
Royal Society United Kingdom
Citation
Journal: 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.
#1: Journal: Ssrn / Year: 2022
Title: Improving the Thermostability of the Geobacillus Pallidus Nitrile Hydratase by Directed Evolution
Authors: Van Wyk, J.C. / Cowan, D.A. / Danson, M.J. / Tsekoa, T.L. / Sayed, M.F. / Sewell, B.T.
History
DepositionFeb 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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)50,3824
Polymers50,2872
Non-polymers942
Water7,692427
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)100,7638
Polymers100,5754
Non-polymers1894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area22470 Å2
ΔGint-124 kcal/mol
Surface area32880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.180, 106.180, 82.880
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
11B-417-

HOH

21B-449-

HOH

31B-508-

HOH

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Components

#1: Protein Nitrile hydratase


Mass: 23755.188 Da / Num. of mol.: 1 / Fragment: chain A / Mutation: S169R
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: 26532.098 Da / Num. of mol.: 1 / Fragment: chain B / Mutation: M43K, T150A
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-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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
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: 1.45→44.69 Å / Num. obs: 83831 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.05 Å2 / Rmerge(I) obs: 0.038 / Χ2: 0.99 / Net I/σ(I): 13.5
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3 / Num. unique obs: 83831 / Χ2: 1.48 / % possible all: 99.9

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Processing

Software
NameVersionClassification
d*TREKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.22data extraction
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dpp

2dpp


Resolution: 1.45→44.69 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.928 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1843 4175 5 %RANDOM
Rwork0.1424 ---
obs0.1444 83659 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 68.62 Å2 / Biso mean: 15.001 Å2 / Biso min: 7.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 1.45→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 2 427 3922
Biso mean--14.65 28.63 -
Num. residues----429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223676
X-RAY DIFFRACTIONr_bond_other_d0.0030.022596
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9684995
X-RAY DIFFRACTIONr_angle_other_deg1.00936300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3825450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52623.222180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8715644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5881531
X-RAY DIFFRACTIONr_chiral_restr0.1210.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02771
X-RAY DIFFRACTIONr_rigid_bond_restr2.29936272
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 284 -
Rwork0.252 5748 -
all-6032 -
obs--98.64 %

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