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- PDB-5jqn: NitN Amidase from Neterenkonia sp. AN1 after thrombin His-tag removal. -

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Basic information

Entry
Database: PDB / ID: 5jqn
TitleNitN Amidase from Neterenkonia sp. AN1 after thrombin His-tag removal.
ComponentsAliphatic amidase
KeywordsHYDROLASE / NitN Amidase / Neterenkonia sp. AN1
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. AN1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsSewell, B.T. / Kimani, S.W. / Weber, B.W.
Citation
Journal: To Be Published
Title: QM/MM Modelling of Substrate Binding in the Amidase Active Site
Authors: Sewell, B.T. / Kimani, S.W. / Venter, G.A. / Hunter, R. / Schell, D.T.
#1: Journal: Appl. Environ. Microbiol. / Year: 2011
Title: Unique aliphatic amidase from a psychrotrophic and haloalkaliphilic nesterenkonia isolate.
Authors: Nel, A.J. / Tuffin, I.M. / Sewell, B.T. / Cowan, D.A.
History
DepositionMay 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aliphatic amidase


Theoretical massNumber of molelcules
Total (without water)28,2441
Polymers28,2441
Non-polymers00
Water3,441191
1
A: Aliphatic amidase

A: Aliphatic amidase


Theoretical massNumber of molelcules
Total (without water)56,4872
Polymers56,4872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3620 Å2
ΔGint-6 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.423, 115.794, 65.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

21A-363-

HOH

31A-370-

HOH

41A-465-

HOH

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Components

#1: Protein Aliphatic amidase


Mass: 28243.664 Da / Num. of mol.: 1 / Mutation: GSH arising from the N-terminal His-tag.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nesterenkonia sp. AN1 (bacteria) / Gene: nit2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C6K3Z5, amidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2M Ammonium Sufate

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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 8, 2015 / Details: Toroidal Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.19→45.566 Å / Num. obs: 91215 / % possible obs: 98.6 % / Redundancy: 5.6 % / Rrim(I) all: 0.037 / Net I/σ(I): 25.13 / Num. measured all: 580951
Reflection shellHighest resolution: 1.19 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HKX

3hkx


Resolution: 1.19→45.566 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1832 2000 2.19 %
Rwork0.1751 --
obs0.1753 91210 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.19→45.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 0 191 2105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062049
X-RAY DIFFRACTIONf_angle_d1.0162819
X-RAY DIFFRACTIONf_dihedral_angle_d20.341784
X-RAY DIFFRACTIONf_chiral_restr0.079311
X-RAY DIFFRACTIONf_plane_restr0.008386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1897-1.21940.28171260.26125650X-RAY DIFFRACTION88
1.2194-1.25240.26421400.22736221X-RAY DIFFRACTION98
1.2524-1.28920.20341440.20146398X-RAY DIFFRACTION100
1.2892-1.33080.22581430.19556368X-RAY DIFFRACTION100
1.3308-1.37840.20051430.18926403X-RAY DIFFRACTION100
1.3784-1.43360.17011430.1826379X-RAY DIFFRACTION100
1.4336-1.49890.1811440.17646398X-RAY DIFFRACTION100
1.4989-1.57790.18781430.16746409X-RAY DIFFRACTION100
1.5779-1.67680.17561450.16596445X-RAY DIFFRACTION100
1.6768-1.80620.18921440.16586410X-RAY DIFFRACTION100
1.8062-1.9880.17731450.16596473X-RAY DIFFRACTION100
1.988-2.27560.16461430.16416440X-RAY DIFFRACTION100
2.2756-2.8670.18441480.17826528X-RAY DIFFRACTION100
2.867-45.59930.17711490.17176688X-RAY DIFFRACTION99

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