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- PDB-3hkx: Crystal structure analysis of an amidase from Nesterenkonia sp. -

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Basic information

Entry
Database: PDB / ID: 3hkx
TitleCrystal structure analysis of an amidase from Nesterenkonia sp.
ComponentsAmidase
KeywordsHYDROLASE / ALPHA-BETA-BETA-ALPHA:ALPHA-BETA-BETA-ALPHA DIMERIC SANDWICH
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 / molecular replacement / Resolution: 1.66 Å
AuthorsSewell, B.T. / Nel, A.J.M. / Cowan, D.A.
Citation
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.
#1: Journal: Thesis / Year: 2009
Title: Isolation of a novel cold-adapted nitrile hydrolysing micro-organism
Authors: Nel, A.J.M.
History
DepositionMay 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 20, 2013Group: Database references / Other
Revision 1.3Sep 6, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)30,1171
Polymers30,1171
Non-polymers00
Water3,495194
1
A: Amidase

A: Amidase


Theoretical massNumber of molelcules
Total (without water)60,2342
Polymers60,2342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3600 Å2
ΔGint-9 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.999, 115.639, 65.321
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Amidase


Mass: 30116.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nesterenkonia sp. 10004 (bacteria) / Strain: AN1 / Gene: Nit2 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: D0VWZ1, amidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Sodium acetate trihydrate and 2M ammonium sulphate, pH 4.6, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9778 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 25, 2009
Details: J. Synchrotron Rad. (1999). 6, 822-833 Development of instrumentation and methods for MAD and structural genomics at the SRS, ESRF, CHESS and Elettra facilities A. Cassetta, A. M. Deacon, S. ...Details: J. Synchrotron Rad. (1999). 6, 822-833 Development of instrumentation and methods for MAD and structural genomics at the SRS, ESRF, CHESS and Elettra facilities A. Cassetta, A. M. Deacon, S. E. Ealick, J. R. Helliwell and A. W. Thompson
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionRedundancy: 7.03 % / Number: 242641 / Rmerge(I) obs: 0.046 / Χ2: 0.94 / D res high: 1.66 Å / D res low: 38 Å / Num. obs: 34232 / % possible obs: 99.6
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
3.583899.50.0240.687.01132
2.843.581000.0440.717.26137
2.482.8499.90.0680.787.26121
2.252.4899.90.0720.797.19130
2.092.2599.70.0870.857.04183
1.972.0999.70.1140.946.96221
1.871.9799.70.1571.036.95171
1.791.8799.40.2251.176.89258
1.721.7999.60.2941.256.87257
1.661.7298.90.3661.336.92210
ReflectionResolution: 1.66→63.511 Å / Num. all: 34246 / Num. obs: 34232 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.03 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 15.6
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 6.92 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 26.9 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38 Å
Translation2.5 Å38 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.1.1phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MxCuBEdata collection
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F89

1f89


Resolution: 1.66→63.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.835 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21433 1727 5 %RANDOM
Rwork0.18566 ---
obs0.18713 32495 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.576 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2--0.38 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.66→63.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 194 2164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222033
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9872777
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5655266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85623.93389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03515306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3111517
X-RAY DIFFRACTIONr_chiral_restr0.1560.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0221598
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.761.51323
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.70422114
X-RAY DIFFRACTIONr_scbond_it3.9653710
X-RAY DIFFRACTIONr_scangle_it6.2384.5663
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 120 -
Rwork0.309 2358 -
obs--99.12 %

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