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- PDB-5ny2: A C145A mutant of Nesterenkonia AN1 amidase from the nitrilase su... -

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Basic information

Entry
Database: PDB / ID: 5ny2
TitleA C145A mutant of Nesterenkonia AN1 amidase from the nitrilase superfamily
ComponentsAmidase
KeywordsHYDROLASE / active site / amidase / cysteine 145 / alanine 145 / nitrilase superfamily
Function / homology
Function and homology information


amidase / indoleacetamide hydrolase activity / N-carbamoylputrescine amidase activity / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity / putrescine biosynthetic process from arginine / amidase activity
Similarity search - Function
(R)-stereoselective amidase RamA-like / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNesterenkonia sp. 10004 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKimani, S.W. / Sewell, B.T.
Funding support South Africa, 1items
OrganizationGrant numberCountry
National Research Foundation South Africa
CitationJournal: To be published
Title: Substrate recognition by an amidase of the nitrilase superfamily
Authors: Kimani, S.W. / Venter, G.A. / Sewell, B.T.
History
DepositionMay 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amidase


Theoretical massNumber of molelcules
Total (without water)28,7031
Polymers28,7031
Non-polymers00
Water2,594144
1
A: Amidase

A: Amidase


Theoretical massNumber of molelcules
Total (without water)57,4062
Polymers57,4062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3610 Å2
ΔGint-7 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.250, 114.328, 65.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

21A-355-

HOH

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Components

#1: Protein Amidase /


Mass: 28703.248 Da / Num. of mol.: 1 / Mutation: C145A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nesterenkonia sp. 10004 (bacteria) / Gene: Nit2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0VWZ1, amidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2.0 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.85→45.673 Å / Num. obs: 24678 / % possible obs: 98.4 % / Redundancy: 7.287 % / Biso Wilson estimate: 31.727 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.059 / Χ2: 1.004 / Net I/σ(I): 24.31 / Num. measured all: 179825
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.967.2810.4314.927681398638020.9650.46495.4
1.96-2.17.4590.2547.9428143377437730.9850.273100
2.1-2.267.3240.17112.625083350534250.9910.18497.7
2.26-2.487.3950.11916.8523006322531110.9960.12896.5
2.48-2.777.4070.07124.921843294929490.9980.076100
2.77-3.27.3460.04735.9519115260226020.9990.051100
3.2-3.917.0670.03451.2215802223822360.9990.03799.9
3.91-5.516.9980.02562.0512211174517450.9990.027100
5.51-45.6736.7060.02163.7869411043103510.02399.2

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Processing

Software
NameVersionClassification
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Undeposited model

Resolution: 1.85→64.01 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.176 / FOM work R set: 0.7616 / SU B: 4.233 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1399 / SU Rfree: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 1245 5 %RANDOM
Rwork0.1986 ---
obs0.2002 23621 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.93 Å2 / Biso mean: 30.232 Å2 / Biso min: 15.94 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.85→64.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 0 144 2105
Biso mean---37.6 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192010
X-RAY DIFFRACTIONr_bond_other_d0.0020.021939
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.9862747
X-RAY DIFFRACTIONr_angle_other_deg1.07534451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0155264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69923.86488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98815301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.631517
X-RAY DIFFRACTIONr_chiral_restr0.110.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212338
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02439
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 88 -
Rwork0.4 1634 -
all-1722 -
obs--94.25 %

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