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- PDB-4c5p: The structure of mycobacterium marinum arylamine n-acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 4c5p
TitleThe structure of mycobacterium marinum arylamine n-acetyltransferase
ComponentsARYLAMINE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE / TUBERCULOSIS
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 / Lipocalin / Papain-like cysteine peptidase superfamily / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / Arylamine N-acetyltransferase Nat
Similarity search - Component
Biological speciesMYCOBACTERIUM MARINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.592 Å
AuthorsAbuhammad, A. / Lowe, E.D. / Garman, E.F. / Sim, E.
CitationJournal: Ph D Thesis
Title: Arylamine N-Acetyltransferases from Mycobacteria: Investigations of a Potential Target for Anti- Tubercular Therapy
Authors: Abuhammad, A.
History
DepositionSep 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Atomic model
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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:
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Assembly

Deposited unit
A: ARYLAMINE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2395
Polymers30,9671
Non-polymers2724
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.750, 51.750, 176.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2221-

HOH

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Components

#1: Protein ARYLAMINE N-ACETYLTRANSFERASE


Mass: 30967.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM MARINUM (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: B2HIZ6, arylamine N-acetyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 1.87 Å3/Da / Density % sol: 34.3 % / Description: NONE
Crystal growDetails: 0.2 M NA2SO4, 0.1 M BIS-TRIS PROPANE PH 6.5 AND 20 % W/V PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.59→38.8 Å / Num. obs: 33245 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 17.11 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.7

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.592→38.82 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 16.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1935 1675 5.1 %
Rwork0.1545 --
obs0.1564 33153 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.7 Å2
Refinement stepCycle: LAST / Resolution: 1.592→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 17 284 2363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012233
X-RAY DIFFRACTIONf_angle_d1.2833057
X-RAY DIFFRACTIONf_dihedral_angle_d13.532800
X-RAY DIFFRACTIONf_chiral_restr0.077350
X-RAY DIFFRACTIONf_plane_restr0.006404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.592-1.63890.28361390.2582554X-RAY DIFFRACTION100
1.6389-1.69180.28011590.22982546X-RAY DIFFRACTION100
1.6918-1.75230.22421370.21572568X-RAY DIFFRACTION100
1.7523-1.82240.2341350.18272576X-RAY DIFFRACTION100
1.8224-1.90540.20521390.15832576X-RAY DIFFRACTION100
1.9054-2.00580.16951270.13292612X-RAY DIFFRACTION100
2.0058-2.13150.16171330.12942597X-RAY DIFFRACTION100
2.1315-2.2960.19381600.12572590X-RAY DIFFRACTION100
2.296-2.5270.17821390.13512625X-RAY DIFFRACTION100
2.527-2.89260.17331320.142666X-RAY DIFFRACTION100
2.8926-3.64390.16391410.13992692X-RAY DIFFRACTION100
3.6439-38.83110.20951340.1662876X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 22.349 Å / Origin y: 1.1728 Å / Origin z: 12.1545 Å
111213212223313233
T0.0651 Å20.01 Å2-0.0022 Å2-0.055 Å2-0.0006 Å2--0.0435 Å2
L0.8541 °2-0 °2-0.0026 °2-0.8879 °2-0.1175 °2--0.8455 °2
S0.007 Å °-0.0763 Å °-0.0268 Å °0.0606 Å °0.0047 Å °-0.0469 Å °0.0465 Å °0.0603 Å °-0.0101 Å °
Refinement TLS groupSelection details: ALL

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