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- PDB-5nz5: A C145S mutant of Nesterenkonia AN1 amidase from the nitrilase su... -

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Basic information

Entry
Database: PDB / ID: 5nz5
TitleA C145S mutant of Nesterenkonia AN1 amidase from the nitrilase superfamily
ComponentsAmidase
KeywordsHYDROLASE / active site / amidase / cysteine 145 / serine 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 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: 1.47 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 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 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

Downloads & links

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Assembly

Deposited unit
A: Amidase


Theoretical massNumber of molelcules
Total (without water)30,0851
Polymers30,0851
Non-polymers00
Water4,035224
1
A: Amidase

A: Amidase


Theoretical massNumber of molelcules
Total (without water)60,1692
Polymers60,1692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3630 Å2
ΔGint-8 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.399, 114.996, 65.589
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-479-

HOH

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Components

#1: Protein Amidase


Mass: 30084.686 Da / Num. of mol.: 1 / Mutation: C145S
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.: 224 / 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: 2.36 Å3/Da / Density % sol: 47.95 % / Mosaicity: 1.14 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M Sodium cacodylate trihydtrate, 30% PEG 8000

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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 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.47→23.646 Å / Num. all: 48675 / Num. obs: 48675 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Rsym value: 0.066 / Net I/av σ(I): 8.2 / Net I/σ(I): 17 / Num. measured all: 337984
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.47-1.556.70.37524700070030.1550.4070.3754.599.9
1.55-1.646.70.2592.94484666970.1070.2810.2596.3100
1.64-1.766.80.1844.14252762590.0760.1990.1848.9100
1.76-1.96.90.1245.84050258410.0510.1340.12412.3100
1.9-2.087.10.0818.53835053950.0330.0880.08117.3100
2.08-2.327.20.0679.63523248870.0270.0730.06721.3100
2.32-2.687.20.0728.43132843400.0280.0770.07225100
2.68-3.297.20.0619.42672137240.0240.0660.06132100
3.29-4.657.10.031192045428810.0130.0340.03144.8100
4.65-23.6466.70.02424.81102416480.010.0260.02442.798.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HKX

3hkx


Resolution: 1.47→22.99 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1595 / WRfactor Rwork: 0.1384 / FOM work R set: 0.9083 / SU B: 0.81 / SU ML: 0.031 / SU R Cruickshank DPI: 0.0514 / SU Rfree: 0.0536 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1632 2509 5.1 %RANDOM
Rwork0.1406 ---
obs0.1417 46228 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.18 Å2 / Biso mean: 14.22 Å2 / Biso min: 5.92 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.47→22.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 0 224 2163
Biso mean---28.28 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192058
X-RAY DIFFRACTIONr_bond_other_d0.0030.021971
X-RAY DIFFRACTIONr_angle_refined_deg2.5611.992825
X-RAY DIFFRACTIONr_angle_other_deg1.22834544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50123.97893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89615315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6441518
X-RAY DIFFRACTIONr_chiral_restr0.1770.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212417
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02449
LS refinement shellResolution: 1.47→1.508 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 183 -
Rwork0.197 3381 -
all-3564 -
obs--99.94 %

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