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- PDB-5ny7: A C145A mutant of Nesterenkonia AN1 amidase bound to nicotinamide -

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Basic information

Entry
Database: PDB / ID: 5ny7
TitleA C145A mutant of Nesterenkonia AN1 amidase bound to nicotinamide
ComponentsAmidase
KeywordsHYDROLASE / active site / amidase / amide / nicotinamide / cysteine 145 / alanine 145 / nitrilase superfamily
Function / homology
Function and homology information


amidase / indoleacetamide hydrolase activity / organonitrogen compound metabolic process / 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
NICOTINAMIDE / Amidase
Similarity search - Component
Biological speciesNesterenkonia sp. 10004 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsKimani, S.W. / Sewell, B.T.
Funding support South Africa, 1items
OrganizationGrant numberCountry
National Research Foundation91532 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 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5035
Polymers30,1011
Non-polymers4024
Water3,873215
1
A: Amidase
hetero molecules

A: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,00510
Polymers60,2012
Non-polymers8048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5040 Å2
ΔGint-24 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.249, 114.779, 65.363
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-430-

HOH

21A-454-

HOH

31A-565-

HOH

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Components

#1: Protein Amidase /


Mass: 30100.686 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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.34 Å3/Da / Density % sol: 47.53 % / Mosaicity: 0.268 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES sodium, 2% PEG 400, 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: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.31→50 Å / Num. obs: 63442 / % possible obs: 93.1 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.046 / Χ2: 1.156 / Net I/σ(I): 11.3 / Num. measured all: 280873
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.31-1.332.20.37918871.136155.6
1.33-1.362.50.31922580.652167.1
1.36-1.382.70.28924800.641174.3
1.38-1.412.90.27227710.665181.9
1.41-1.443.30.25429660.695188.5
1.44-1.483.70.23632450.775195.5
1.48-1.514.60.21833540.818199.6
1.51-1.554.90.17134090.7761100
1.55-1.64.90.16633460.8181100
1.6-1.654.90.12833720.7861100
1.65-1.714.90.10134060.7751100
1.71-1.784.90.08733780.8211100
1.78-1.864.90.07234110.8471100
1.86-1.9650.0634040.9261100
1.96-2.0850.04934060.9931100
2.08-2.2450.04333961.0781100
2.24-2.4750.04334341.3221100
2.47-2.8250.05634422.4681100
2.82-3.564.90.04334872.4731100
3.56-504.80.02335902.126199

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HKX

3hkx


Resolution: 1.31→30.24 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1758 / WRfactor Rwork: 0.1499 / FOM work R set: 0.8946 / SU B: 0.646 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0429 / SU Rfree: 0.0459 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / 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
Rfree0.1743 3218 5.1 %RANDOM
Rwork0.1505 ---
obs0.1517 60208 93.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.94 Å2 / Biso mean: 14.738 Å2 / Biso min: 5.41 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.31→30.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 28 215 2200
Biso mean--21.61 27.63 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0192068
X-RAY DIFFRACTIONr_bond_other_d0.0030.021976
X-RAY DIFFRACTIONr_angle_refined_deg2.6182.0032832
X-RAY DIFFRACTIONr_angle_other_deg1.19134536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4815272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59324.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37215304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.671516
X-RAY DIFFRACTIONr_chiral_restr0.170.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212424
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02467
LS refinement shellResolution: 1.311→1.345 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 166 -
Rwork0.236 2853 -
all-3019 -
obs--60.4 %

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