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- PDB-1w6f: Arylamine N-acetyltransferase from Mycobacterium smegmatis with t... -

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Basic information

Entry
Database: PDB / ID: 1w6f
TitleArylamine N-acetyltransferase from Mycobacterium smegmatis with the anti-tubercular drug isoniazid bound in the active site.
ComponentsARYLAMINE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE / NAT / TUBERCULOSIS / ACETYLTRANSFERASE
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
4-(DIAZENYLCARBONYL)PYRIDINE / Arylamine N-acetyltransferase
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSandy, J. / Holton, S. / Fullham, E. / Sim, E. / Noble, M.E.M.
CitationJournal: Protein Sci. / Year: 2005
Title: Binding of the Anti-Tubercular Drug Isoniazid to the Arylamine N-Acetyltransferase Protein from Mycobacterium Smegmatis
Authors: Sandy, J. / Holton, S. / Fullham, E. / Sim, E. / Noble, M.E.M.
History
DepositionAug 17, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2005Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,8068
Polymers122,2654
Non-polymers5404
Water12,935718
1
A: ARYLAMINE N-ACETYLTRANSFERASE
B: ARYLAMINE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4034
Polymers61,1332
Non-polymers2702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: ARYLAMINE N-ACETYLTRANSFERASE
D: ARYLAMINE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4034
Polymers61,1332
Non-polymers2702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.208, 106.039, 140.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ARYLAMINE N-ACETYLTRANSFERASE


Mass: 30566.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: ISONIAZID / Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O86309, arylamine N-acetyltransferase
#2: Chemical
ChemComp-ISZ / 4-(DIAZENYLCARBONYL)PYRIDINE / ISONIAZID / TUBAZID / RIMITSID / ISONICOTINYLHYDRAZINE / LANIZID / NYDRAZID


Mass: 135.123 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5N3O / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOULD HAVE A ROLE IN ACETYLATING, AND HENCE INACTIVATING, THE ANTITUBERCULAR DRUG ISONIAZID.

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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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.5
Details: 0.2M AMMONIUM SULPHATE, 0.1M MES PH 6.5, 30% PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.39→31.62 Å / Num. obs: 84858 / % possible obs: 92.2 % / Observed criterion σ(I): 3 / Redundancy: 3.34 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.17
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.16 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GX3 CHAIN A

1gx3


Resolution: 2.1→84.52 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / σ(F): 2.1 / ESU R: 0.187 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 4104 5 %RANDOM
Rwork0.18 ---
obs0.182 107157 92.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 23.94 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å20 Å2
2---0.01 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→84.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8408 0 40 718 9166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0218640
X-RAY DIFFRACTIONr_bond_other_d00.027918
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.95311770
X-RAY DIFFRACTIONr_angle_other_deg3.735318174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98951079
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.21305
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029881
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021895
X-RAY DIFFRACTIONr_nbd_refined0.2450.21638
X-RAY DIFFRACTIONr_nbd_other0.3110.28736
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1070.24494
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2625
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3830.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1681.55363
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12928609
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.93233277
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8814.53161
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: 2→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 314
Rwork0.227 5584

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