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- PDB-1gx3: M. smegmatis arylamine N-acetyl transferase -

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Basic information

Entry
Database: PDB / ID: 1gx3
TitleM. smegmatis arylamine N-acetyl transferase
ComponentsARYLAMINE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE / DRUG METABOLISM / MYCOBACTERIA / ISONIAZID / ARYLAMINE N- ACETYLTRANSFERASE / NAT
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: 1.7 Å
AuthorsSandy, J. / Mushtaq, A. / Kawamura, A. / Sinclair, J. / Sim, E. / Noble, M.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The Structure of Arylamine N-Acetyltransferase from Mycobacterium Smegmatis-an Enzyme which Inactivates the Anti-Tubercular Drug, Isoniazid
Authors: Sandy, J. / Mushtaq, A. / Kawamura, A. / Sinclair, J. / Sim, E. / Noble, M.
History
DepositionMar 26, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARYLAMINE N-ACETYLTRANSFERASE
B: ARYLAMINE N-ACETYLTRANSFERASE
C: ARYLAMINE N-ACETYLTRANSFERASE
D: ARYLAMINE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)125,2014
Polymers125,2014
Non-polymers00
Water13,601755
1
A: ARYLAMINE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)31,3001
Polymers31,3001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ARYLAMINE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)31,3001
Polymers31,3001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ARYLAMINE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)31,3001
Polymers31,3001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ARYLAMINE N-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)31,3001
Polymers31,3001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.250, 105.828, 141.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.89243, -0.45101, 0.01239), (-0.45085, -0.89249, -0.0138), (0.01729, 0.00673, -0.99983)1.04546, 12.04726, 85.10079
2given(0.97246, 0.22861, -0.04544), (-0.22936, 0.97327, -0.01199), (0.04148, 0.02208, 0.9989)1.45327, 57.86871, 15.79933
3given(0.75659, -0.65323, -0.02929), (-0.65377, -0.75483, -0.05318), (0.01263, 0.05939, -0.99816)4.46386, 71.33519, 101.89999
4given(0.76423, -0.64178, 0.06376), (-0.64373, -0.76511, 0.0145), (0.03948, -0.05213, -0.99786)2.96009, 66.52236, 101.30556
5given(0.96944, 0.2424, 0.03785), (-0.24376, 0.96914, 0.03678), (-0.02776, -0.04488, 0.99861)-2.69115, 56.78486, 17.48737
6given(0.58771, -0.80898, -0.01225), (-0.80593, -0.58402, -0.09689), (0.07123, 0.06681, -0.99522)50.61787, 107.83356, 113.65443

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Components

#1: Protein
ARYLAMINE N-ACETYLTRANSFERASE / N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE


Mass: 31300.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: (HIS)6 AND 3 RESIDUES INTRODUCED BEFORE AUTHENTIC STARTING METHIONINE AS CLONING ARTEFACTS
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Plasmid: PET-28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O86309, arylamine N-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 755 / Source method: isolated from a natural source / Formula: H2O
Sequence details(HIS)6 TAG AND 3 N-TERMINAL RESIDUES ARE CLONING ARTEFACT

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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: 3.02 Å3/Da / Density % sol: 52 %
Crystal growpH: 8.5
Details: 0.2 M NH4 ACETATE, 0.1M TRIS-HCL PH 8.5, 30%V/V ISOPROPANOL
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
220 mMTris-HCl1drop
31 mMEDTA1drop
42 mMdithiothreitol1droppH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: QUANTUM ADSC / Detector: CCD / Date: Feb 19, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→84 Å / Num. obs: 163227 / % possible obs: 98 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 3.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 1.3 / % possible all: 87.4
Reflection
*PLUS
Lowest resolution: 84 Å / % possible obs: 98.1 % / Num. measured all: 624263 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 87.4 % / Num. unique obs: 14137 / Num. measured obs: 34821 / Rmerge(I) obs: 0.568

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E2T

1e2t


Resolution: 1.7→30 Å / SU B: 6.557 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R Free: 0.103 / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.241 8187 5 %RANDOM
Rwork0.209 ---
obs0.211 155013 98 %-
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8508 0 0 755 9263
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor all: 0.211 / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.967
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.74 Å / Rfactor Rfree: 0.338 / Rfactor Rwork: 0.276 / Num. reflection Rwork: 514 / Total num. of bins used: 20 / Rfactor obs: 0.276

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