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

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Basic information

Entry
Database: PDB / ID: 5nxz
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 / N-carbamoylputrescine amidase 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 domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNesterenkonia sp. 10004 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 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 2.0May 1, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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)30,0691
Polymers30,0691
Non-polymers00
Water3,855214
1
A: Amidase

A: Amidase


Theoretical massNumber of molelcules
Total (without water)60,1372
Polymers60,1372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3750 Å2
ΔGint-13 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.814, 114.977, 65.827
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-356-

HOH

21A-470-

HOH

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Components

#1: Protein Amidase


Mass: 30068.686 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.35 Å3/Da / Density % sol: 47.75 %
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: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.21→57.49 Å / Num. obs: 82613 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 6.668 % / Biso Wilson estimate: 17.776 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.052 / Χ2: 0.948 / Net I/σ(I): 20.21 / Num. measured all: 550851
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
1.21-1.286.2830.4654.117360513856117150.8870.50684.5
1.28-1.376.8590.3116.588561013048124810.9570.33695.7
1.37-1.486.5350.1959.687713412154118030.980.21197.1
1.48-1.626.9390.11315.737582211177109270.9930.12297.8
1.62-1.816.9150.07122.886964410187100710.9970.07798.9
1.81-2.096.3440.04531.2555349899187240.9980.0597
2.09-2.566.9350.03741.1652914766476300.9990.04199.6
2.56-3.626.510.03445.4538769599359550.9980.03799.4
3.62-57.496.6540.03750.0722004343533070.9980.04196.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Undeposited model

Resolution: 1.21→57.49 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.2008 / WRfactor Rwork: 0.1688 / FOM work R set: 0.8772 / SU B: 0.563 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0365 / SU Rfree: 0.0402 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 1997 2.4 %RANDOM
Rwork0.1682 ---
obs0.1688 80620 95.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.71 Å2 / Biso mean: 14.849 Å2 / Biso min: 6.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.21→57.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 0 214 2161
Biso mean---26.4 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0192042
X-RAY DIFFRACTIONr_bond_other_d0.0030.021957
X-RAY DIFFRACTIONr_angle_refined_deg2.6251.992802
X-RAY DIFFRACTIONr_angle_other_deg1.24734504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4765273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35224.04589
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42815304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1491516
X-RAY DIFFRACTIONr_chiral_restr0.1860.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212396
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02444
LS refinement shellResolution: 1.21→1.242 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 120 -
Rwork0.264 4812 -
all-4932 -
obs--77.74 %

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