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- PDB-5nyb: A C145A mutant of Nesterenkonia AN1 amidase bound to adipamide -

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Basic information

Entry
Database: PDB / ID: 5nyb
TitleA C145A mutant of Nesterenkonia AN1 amidase bound to adipamide
ComponentsAmidase
KeywordsHYDROLASE / active site / amidase / amide / adipamide / 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: 1.88 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 1.0Jun 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

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Assembly

Deposited unit
A: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2132
Polymers30,0691
Non-polymers1441
Water1,11762
1
A: Amidase
hetero molecules

A: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4264
Polymers60,1372
Non-polymers2882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3580 Å2
ΔGint-11 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.254, 114.769, 64.842
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-417-

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: Chemical ChemComp-9EE / adipamide


Mass: 144.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 47.86 % / Mosaicity: 0.832 °
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: May 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.88→100 Å / Num. obs: 23407 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Χ2: 1.088 / Net I/σ(I): 6.4 / Num. measured all: 106081
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.88-1.914.40.5611400.68198.3
1.91-1.954.50.44111240.744198.8
1.95-1.984.60.42511370.734199
1.98-2.034.50.3511740.76199.7
2.03-2.074.60.30111340.836199.9
2.07-2.124.60.27511670.843199.8
2.12-2.174.60.27611650.8121100
2.17-2.234.60.23611540.8731100
2.23-2.294.60.21211660.791100
2.29-2.374.60.17111670.8291100
2.37-2.454.60.17111730.843199.9
2.45-2.554.60.15311680.832199.9
2.55-2.674.60.12111540.8641100
2.67-2.814.60.10911740.9071100
2.81-2.984.60.09711821.1531100
2.98-3.214.50.09111721.7111100
3.21-3.544.50.08211842.1641100
3.54-4.054.50.06312002.1621100
4.05-5.14.40.04612041.5991100
5.1-1004.20.04112681.569198.8

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Processing

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

3hkx


Resolution: 1.88→32.87 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.1462 / FOM work R set: 0.8304 / SU B: 3.446 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1229 / SU Rfree: 0.1252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1199 5.1 %RANDOM
Rwork0.1679 ---
obs0.1702 22154 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.77 Å2 / Biso mean: 26.398 Å2 / Biso min: 14.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.88→32.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 10 62 2033
Biso mean--32.82 32.96 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192019
X-RAY DIFFRACTIONr_bond_other_d0.0020.021948
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.9892757
X-RAY DIFFRACTIONr_angle_other_deg1.0293.0034474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1175264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6823.86488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63315301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8731517
X-RAY DIFFRACTIONr_chiral_restr0.1150.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212344
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02441
LS refinement shellResolution: 1.881→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 100 -
Rwork0.265 1497 -
all-1597 -
obs--93.56 %

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