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- PDB-5nyc: A C145A mutant of Nesterenkonia AN1 amidase bound to propionitrile -

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Basic information

Entry
Database: PDB / ID: 5nyc
TitleA C145A mutant of Nesterenkonia AN1 amidase bound to propionitrile
ComponentsAmidase
KeywordsHYDROLASE / active site / amidase / nitrile / propionitrile / 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
propanenitrile / DI(HYDROXYETHYL)ETHER / Amidase
Similarity search - Component
Biological speciesNesterenkonia sp. 10004 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4466
Polymers30,0691
Non-polymers3775
Water3,693205
1
A: Amidase
hetero molecules

A: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,89212
Polymers60,1372
Non-polymers75510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4440 Å2
ΔGint-6 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.469, 115.492, 65.192
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-421-

HOH

21A-513-

HOH

31A-563-

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) / Strain (production host): BL21(DE3) / References: UniProt: D0VWZ1, amidase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CNV / propanenitrile


Mass: 55.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 47.93 % / Mosaicity: 0.52 °
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: Nov 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.51→28.43 Å / Num. all: 44728 / Num. obs: 44728 / % possible obs: 99.6 % / Redundancy: 7.4 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.073 / Rsym value: 0.067 / Net I/av σ(I): 7.2 / Net I/σ(I): 18.5 / Num. measured all: 331475
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
1.51-1.597.40.36824728763940.1440.3960.3685.499.1
1.59-1.697.40.2622.84547461100.1020.2810.2627.299.3
1.69-1.87.50.1764.34289357480.0690.1890.17610.199.4
1.8-1.957.50.1156.43998353620.0450.1230.11514.399.7
1.95-2.147.50.07993706849700.0310.0850.07919.999.8
2.14-2.397.50.06310.63373545190.0250.0670.06324.399.9
2.39-2.767.40.05711.12977940050.0220.0620.05727.799.9
2.76-3.387.40.05710.32516034040.0220.0610.05733.5100
3.38-4.787.30.04412.81953626920.0170.0480.04443.2100
4.78-28.4126.90.03316.91056015240.0130.0360.03343.198.9

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Processing

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

3hkx


Resolution: 1.51→28.43 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1651 / WRfactor Rwork: 0.138 / FOM work R set: 0.8976 / SU B: 0.97 / SU ML: 0.036 / SU R Cruickshank DPI: 0.057 / SU Rfree: 0.0602 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.171 2280 5.1 %RANDOM
Rwork0.144 ---
obs0.1454 42531 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.32 Å2 / Biso mean: 15.138 Å2 / Biso min: 6.62 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.51→28.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 26 205 2178
Biso mean--32.69 29.43 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0192067
X-RAY DIFFRACTIONr_bond_other_d0.0030.021998
X-RAY DIFFRACTIONr_angle_refined_deg2.4441.9972826
X-RAY DIFFRACTIONr_angle_other_deg1.2493.0014579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54924.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77415307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6091516
X-RAY DIFFRACTIONr_chiral_restr0.1630.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212402
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02442
LS refinement shellResolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 157 -
Rwork0.215 3051 -
all-3208 -
obs--98.25 %

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