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- PDB-1w5r: X-ray crystallographic structure of a C70Q Mycobacterium smegmati... -

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Basic information

Entry
Database: PDB / ID: 1w5r
TitleX-ray crystallographic structure of a C70Q Mycobacterium smegmatis N- arylamine Acetyltransferase
ComponentsARYLAMINE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE / ACYLTRANSFERASE
Function / homology
Function and homology information


arylamine N-acetyltransferase / arylamine N-acetyltransferase activity
Similarity search - Function
Arylamine N-acetyltransferase / Cysteine proteinases / Arylamine N-acetyltransferase fold / Arylamine N-acetyltransferase / N-acetyltransferase / Papain-like cysteine peptidase superfamily / Lipocalin / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Arylamine N-acetyltransferase
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHolton, S.J. / Sandy, J. / Rodrigues-Lima, F. / Dupret, J.-M. / Bhakta, S. / Noble, M.E.M. / Sim, E.
CitationJournal: Biochem.J. / Year: 2005
Title: Investigation of the Catalytic Triad of Arylamine N-Acetyltransferases: Essential Residues Required for Acetyl Transfer to Arylamines.
Authors: Sandy, J. / Mushtaq, A. / Holton, S.J. / Schartau, P. / Noble, M.E.M. / Sim, E.
History
DepositionAug 9, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 18, 2020Group: Other / Structure summary / Category: pdbx_database_status / struct / Item: _pdbx_database_status.status_code_sf / _struct.title
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ARYLAMINE N-ACETYLTRANSFERASE
B: ARYLAMINE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)61,1832
Polymers61,1832
Non-polymers00
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.884, 98.884, 130.815
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ARYLAMINE N-ACETYLTRANSFERASE


Mass: 30591.309 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O86309, arylamine N-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION CYS 70 GLU CHAINS A AND B.
Sequence detailsTHE PROTEIN IS PURIFIED USING AN N-TERMINAL HIS-TAG, WHICH IS CLEAVED OFF PRIOR TO CRYSTALLIZATION. ...THE PROTEIN IS PURIFIED USING AN N-TERMINAL HIS-TAG, WHICH IS CLEAVED OFF PRIOR TO CRYSTALLIZATION. THROMBIN CLEAVAGE REMOVES AN INCOMPLETE FRAGMENT OF THE HIS-TAG, LEAVING THREE RESIDUES ATTACHED TO THE INTENDED PROTEIN SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.93 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.3→31.01 Å / Num. obs: 103538 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 3.19 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.79
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 2.72 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.77 / % possible all: 84.7

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 24/04/2001 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→79.06 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.401 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.073 / Stereochemistry target values: MLF / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 5150 4.982 %RANDOM
Rwork0.196 ---
obs0.197 103379 90 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.45→79.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 0 398 4642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214340
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9565916
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9185544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44622.315216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50415656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0061552
X-RAY DIFFRACTIONr_chiral_restr0.0810.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023420
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21944
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22907
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2377
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.981.52768
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52724342
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.97731749
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8044.51574
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: 1.45→1.49 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 316
Rwork0.257 6734

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