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- PDB-2vfb: The structure of Mycobacterium marinum arylamine N-acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 2vfb
TitleThe structure of Mycobacterium marinum arylamine N-acetyltransferase
ComponentsARYLAMINE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE / ARYLAMINE N-ACETYLTRANSFERASE / NAT / ACETYL COA / MYCOBACTERIA / ACTYLTRANSFERASE
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
Arylamine N-acetyltransferase Nat
Similarity search - Component
Biological speciesMYCOBACTERIUM MARINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFullam, E. / Westwood, I.M. / Anderton, M.C. / Lowe, E.D. / Sim, E. / Noble, M.E.M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Divergence of Cofactor Recognition Across Evolution: Coenzyme a Binding in a Prokaryotic Arylamine N-Acetyltransferase.
Authors: Fullam, E. / Westwood, I.M. / Anderton, M.C. / Lowe, E.D. / Sim, E. / Noble, M.E.M.
History
DepositionNov 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 28, 2012Group: Other
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


Theoretical massNumber of molelcules
Total (without water)30,6691
Polymers30,6691
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.526, 51.526, 175.299
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: 30668.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM MARINUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: B2HIZ6*PLUS, arylamine N-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL HIS TAG ADDED

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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: 1.86 Å3/Da / Density % sol: 33.9 % / Description: NONE
Crystal growpH: 7.5
Details: 200MM CACL2, 100MM HEPES, PH7.5, 28% POLY(ETHYLENE GLYCOL) 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.45→51.5 Å / Num. obs: 16884 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 9.24 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GX3

1gx3


Resolution: 2→29.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.934 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 859 5.1 %RANDOM
Rwork0.189 ---
obs0.191 16072 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 0 139 2234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222137
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9652912
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1365270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96822.42499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88815329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.571524
X-RAY DIFFRACTIONr_chiral_restr0.1330.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021652
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2968
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21438
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0471.51375
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64422156
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7663860
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1854.5756
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→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 66
Rwork0.189 1140
Refinement TLS params.Method: refined / Origin x: 22.349 Å / Origin y: 1.374 Å / Origin z: 12.132 Å
111213212223313233
T-0.0836 Å20.0256 Å2-0.008 Å2--0.0958 Å20.0029 Å2---0.0494 Å2
L1.3756 °20.4681 °20.0078 °2-1.8721 °2-0.0362 °2--1.5236 °2
S0.0359 Å °-0.0987 Å °-0.0518 Å °0.1322 Å °-0.0209 Å °-0.0727 Å °0.0819 Å °0.0629 Å °-0.015 Å °

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