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- PDB-4izu: The E41Q mutant of the amidase from Nesterenkonia sp. AN1 showing... -

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Basic information

Entry
Database: PDB / ID: 4izu
TitleThe E41Q mutant of the amidase from Nesterenkonia sp. AN1 showing the result of Michael addition of acrylamide at the active site cysteine
ComponentsAmidase
KeywordsHYDROLASE / propionamide / acrylamide (prop-2-enamide) / cysteine 145
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 superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
prop-2-enamide / PROPIONAMIDE / Amidase
Similarity search - Component
Biological speciesNesterenkonia sp. 10004 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsKimani, S.W. / Sewell, B.T.
CitationJournal: To be Published
Title: Covalent modifications of the active site cysteine occur as a result of mutating the glutamate of the catalytic triad in the amidase from Nesterenkonia sp.
Authors: Kimani, S.W. / Hunter, R. / Vlok, M. / Watermeyer, J. / Sewell, B.T.
History
DepositionJan 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Other
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)30,3174
Polymers30,1001
Non-polymers2173
Water5,639313
1
A: Amidase
hetero molecules

A: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6348
Polymers60,2002
Non-polymers4356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4660 Å2
ΔGint-20 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.102, 115.452, 65.933
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-523-

HOH

21A-687-

HOH

31A-698-

HOH

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Components

#1: Protein Amidase


Mass: 30099.768 Da / Num. of mol.: 1 / Mutation: Q41E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nesterenkonia sp. 10004 (bacteria) / Strain: AN1 / Gene: Nit2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VWZ1, amidase
#2: Chemical ChemComp-ROP / PROPIONAMIDE


Mass: 73.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO
#3: Chemical ChemComp-1HC / prop-2-enamide


Mass: 71.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 298 K
Details: 0.2 M ammonium tartrate dibasic, 20% PEG 3350, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→38.05 Å / Num. obs: 57302 / % possible obs: 99.5 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.8
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.2 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 23.78 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.05 Å
Translation2.5 Å38.05 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.7Ldata reduction
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→38.05 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.819 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0555 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2909 5.1 %RANDOM
Rwork0.173 ---
obs0.174 57295 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 15 313 2235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0222027
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4811.9882766
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1625262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61223.85496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63715316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7531519
X-RAY DIFFRACTIONr_chiral_restr0.1950.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0221604
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_it1.5071.51285
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.43822064
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3243742
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1364.5697
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 204 -
Rwork0.284 3963 -
obs--98.58 %

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