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- PDB-5nye: A C145A mutant of Nesterenkonia AN1 amidase bound to propionamide -

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Basic information

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


indoleacetamide hydrolase activity / 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
DI(HYDROXYETHYL)ETHER / PROPIONAMIDE / Amidase
Similarity search - Component
Biological speciesNesterenkonia sp. 10004 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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

Downloads & links

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Assembly

Deposited unit
A: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4636
Polymers30,0691
Non-polymers3945
Water4,143230
1
A: Amidase
hetero molecules

A: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,92512
Polymers60,1372
Non-polymers78810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5990 Å2
ΔGint-38 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.102, 115.306, 65.348
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-434-

HOH

21A-451-

HOH

31A-562-

HOH

41A-579-

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-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 73.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 47.72 % / Mosaicity: 1.18 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES sodium, 2% PEG 400, 2.0M 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 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.55→23.63 Å / Num. all: 41219 / Num. obs: 41219 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Rsym value: 0.068 / Net I/av σ(I): 8.4 / Net I/σ(I): 17.1 / Num. measured all: 273901
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
1.55-1.6360.4211.83573659200.1810.460.4214.498.8
1.63-1.736.20.2852.73450455970.1220.310.2856.299.3
1.73-1.856.30.2023.83337152860.0850.220.2028.699.5
1.85-26.60.1275.93287449630.0520.1380.1271399.7
2-2.196.90.0868.63163345680.0350.0930.08617.999.8
2.19-2.457.10.065112985841800.0260.0710.06522.199.9
2.45-2.837.20.06410.12640736730.0250.0690.06425.799.9
2.83-3.477.20.05810.12256531540.0230.0630.05832.699.9
3.47-4.97.10.03217.31748124720.0130.0350.03242.4100
4.9-24.4536.70.0229.6947214060.0080.0220.0240.299

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Processing

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

3hkx


Resolution: 1.55→23.63 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1596 / WRfactor Rwork: 0.1367 / FOM work R set: 0.8956 / SU B: 1.091 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0612 / SU Rfree: 0.0628 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1671 2135 5.1 %RANDOM
Rwork0.1432 ---
obs0.1444 39363 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.88 Å2 / Biso mean: 14.9 Å2 / Biso min: 5.96 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.55→23.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 25 230 2208
Biso mean--34.05 28.36 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0192047
X-RAY DIFFRACTIONr_bond_other_d0.0040.021979
X-RAY DIFFRACTIONr_angle_refined_deg2.4051.9982793
X-RAY DIFFRACTIONr_angle_other_deg1.1683.0014527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4545269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29624.06691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62315306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8791517
X-RAY DIFFRACTIONr_chiral_restr0.1560.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212377
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02448
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 148 -
Rwork0.206 2876 -
all-3024 -
obs--99.7 %

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