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- PDB-4guz: Structure of the arylamine N-acetyltransferase from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 4guz
TitleStructure of the arylamine N-acetyltransferase from Mycobacterium abscessus
ComponentsProbable arylamine n-acetyl transferase
KeywordsTRANSFERASE / Acetyltransf_2 Transferase / Acetyltransferase / Acetyl CoenzymeA / Cytosol
Function / homology
Function and homology information


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
Probable arylamine n-acetyl transferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKubiak, X. / Li de la Sierra-Gallay, I. / Haouz, A. / Weber, P. / Rodrigues-Lima, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural and functional characterization of an arylamine N-acetyltransferase from the pathogen Mycobacterium abscessus: differences from other mycobacterial isoforms and implications for selective inhibition.
Authors: Cocaign, A. / Kubiak, X. / Xu, X. / Garnier, G. / Li de la Sierra-Gallay, I. / Chi-Bui, L. / Dairou, J. / Busi, F. / Abuhammad, A. / Haouz, A. / Dupret, J.M. / Herrmann, J.L. / Rodrigues-Lima, F.
History
DepositionAug 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details
Revision 1.2Sep 13, 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
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: Probable arylamine n-acetyl transferase
B: Probable arylamine n-acetyl transferase
C: Probable arylamine n-acetyl transferase
D: Probable arylamine n-acetyl transferase


Theoretical massNumber of molelcules
Total (without water)126,9234
Polymers126,9234
Non-polymers00
Water4,774265
1
A: Probable arylamine n-acetyl transferase


Theoretical massNumber of molelcules
Total (without water)31,7311
Polymers31,7311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable arylamine n-acetyl transferase


Theoretical massNumber of molelcules
Total (without water)31,7311
Polymers31,7311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable arylamine n-acetyl transferase


Theoretical massNumber of molelcules
Total (without water)31,7311
Polymers31,7311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Probable arylamine n-acetyl transferase


Theoretical massNumber of molelcules
Total (without water)31,7311
Polymers31,7311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Probable arylamine n-acetyl transferase
D: Probable arylamine n-acetyl transferase


Theoretical massNumber of molelcules
Total (without water)63,4622
Polymers63,4622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-14 kcal/mol
Surface area24160 Å2
MethodPISA
6
B: Probable arylamine n-acetyl transferase

B: Probable arylamine n-acetyl transferase


Theoretical massNumber of molelcules
Total (without water)63,4622
Polymers63,4622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Buried area1820 Å2
ΔGint-13 kcal/mol
Surface area24120 Å2
MethodPISA
7
C: Probable arylamine n-acetyl transferase

C: Probable arylamine n-acetyl transferase


Theoretical massNumber of molelcules
Total (without water)63,4622
Polymers63,4622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1820 Å2
ΔGint-14 kcal/mol
Surface area24250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.669, 78.763, 175.976
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Probable arylamine n-acetyl transferase


Mass: 31730.840 Da / Num. of mol.: 4 / Fragment: Acetyltransferase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / Gene: MAB_0013c / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: B1ME52, N-hydroxyarylamine O-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 15% PEG 6000, 5% Glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.984 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2011 / Details: COLLIMATING (M1) AND TOROIDAL (M2)MIRRORS
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.8→38.39 Å / Num. all: 98903 / Num. obs: 98775 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.075 % / Biso Wilson estimate: 24.63 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 16.4
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.055 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2.26 / Num. unique all: 15638 / % possible all: 97.6

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D9W

3d9w


Resolution: 1.8→38.39 Å / Cor.coef. Fo:Fc: 0.9429 / Cor.coef. Fo:Fc free: 0.9243 / SU R Cruickshank DPI: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
Details: ADDITIONAL RESTRAINT DICTIONNARY FILE USED THROUGH THE GELLY MODULE IMPLEMENTED IN BUSTER: PROTGEO_OPTION_CHIRALRESTRAINT_FROM_EQUILIB.DAT
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 4914 4.99 %RANDOM
Rwork0.2097 ---
obs0.2115 98458 98.9 %-
all-98903 --
Displacement parametersBiso mean: 27.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.3784 Å20 Å2-0.0014 Å2
2--0.5037 Å20 Å2
3----0.8821 Å2
Refine analyzeLuzzati coordinate error obs: 0.252 Å
Refinement stepCycle: LAST / Resolution: 1.8→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8964 0 0 265 9229
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099195HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9512515HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4143SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes2082
X-RAY DIFFRACTIONt_gen_planes1372HARMONIC5
X-RAY DIFFRACTIONt_it9195HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion2.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1144SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10422SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2336 337 4.69 %
Rwork0.2182 6854 -
all0.219 7191 -
obs-7191 98.9 %

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