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- PDB-4bgf: The 3D-structure of arylamine-N-acetyltransferase from M. tuberculosis -

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Basic information

Entry
Database: PDB / ID: 4bgf
TitleThe 3D-structure of arylamine-N-acetyltransferase from M. tuberculosis
ComponentsARYLAMINE N-ACETYLTRANSFERASE NAT
KeywordsTRANSFERASE / DRUG DESIGN / CROSS-SEEDING / MICRO-SEEDING / MICROSEED MATRIX SCREEN
Function / homologyArylamine N-acetyltransferase / Cysteine proteinases / Arylamine N-acetyltransferase fold / Lipocalin / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta / :
Function and homology information
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsAbuhammad, A. / Lowe, E.D. / McDonough, M.A. / Shaw Stewart, P.D. / Kolek, S.A. / Sim, E. / Garman, E.F.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: Structure of arylamine N-acetyltransferase from Mycobacterium tuberculosis determined by cross-seeding with the homologous protein from M. marinum: triumph over adversity.
Authors: Abuhammad, A. / Lowe, E.D. / McDonough, M.A. / Shaw Stewart, P.D. / Kolek, S.A. / Sim, E. / Garman, E.F.
History
DepositionMar 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Atomic model / Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Nov 13, 2013Group: Atomic model
Revision 1.4Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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 NAT
B: ARYLAMINE N-ACETYLTRANSFERASE NAT
C: ARYLAMINE N-ACETYLTRANSFERASE NAT
D: ARYLAMINE N-ACETYLTRANSFERASE NAT
E: ARYLAMINE N-ACETYLTRANSFERASE NAT
F: ARYLAMINE N-ACETYLTRANSFERASE NAT
G: ARYLAMINE N-ACETYLTRANSFERASE NAT
H: ARYLAMINE N-ACETYLTRANSFERASE NAT


Theoretical massNumber of molelcules
Total (without water)248,5058
Polymers248,5058
Non-polymers00
Water17,997999
1
A: ARYLAMINE N-ACETYLTRANSFERASE NAT


Theoretical massNumber of molelcules
Total (without water)31,0631
Polymers31,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ARYLAMINE N-ACETYLTRANSFERASE NAT


Theoretical massNumber of molelcules
Total (without water)31,0631
Polymers31,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ARYLAMINE N-ACETYLTRANSFERASE NAT


Theoretical massNumber of molelcules
Total (without water)31,0631
Polymers31,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ARYLAMINE N-ACETYLTRANSFERASE NAT


Theoretical massNumber of molelcules
Total (without water)31,0631
Polymers31,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ARYLAMINE N-ACETYLTRANSFERASE NAT


Theoretical massNumber of molelcules
Total (without water)31,0631
Polymers31,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ARYLAMINE N-ACETYLTRANSFERASE NAT


Theoretical massNumber of molelcules
Total (without water)31,0631
Polymers31,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: ARYLAMINE N-ACETYLTRANSFERASE NAT


Theoretical massNumber of molelcules
Total (without water)31,0631
Polymers31,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: ARYLAMINE N-ACETYLTRANSFERASE NAT


Theoretical massNumber of molelcules
Total (without water)31,0631
Polymers31,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.494, 139.147, 96.506
Angle α, β, γ (deg.)90.00, 91.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ARYLAMINE N-ACETYLTRANSFERASE NAT / ARYLAMINE N-ACETYLTRANSFERASE


Mass: 31063.119 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PVLT31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): T7 EXPRESS / References: UniProt: I6XHK1, arylamine N-acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growDetails: 0.02 M CACL2, 0.1 M NA-ACETATE PH 4.6 AND 30 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: MARRESEARCH MARMOSAIC 300MM / Detector: CCD / Date: Jul 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
Reflection twinOperator: L,-K,H / Fraction: 0.57
ReflectionResolution: 2.097→29.6 Å / Num. obs: 136366 / % possible obs: 92.1 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.5
Reflection shellResolution: 2.097→2.2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.8 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
xia2data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LTW

3ltw


Resolution: 2.097→29.629 Å / σ(F): 1.35 / Phase error: 31.61 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1873 7211 5.3 %
Rwork0.1607 --
obs0.1628 136337 91.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.097→29.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16542 0 0 999 17541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01516925
X-RAY DIFFRACTIONf_angle_d1.49623151
X-RAY DIFFRACTIONf_dihedral_angle_d13.8826009
X-RAY DIFFRACTIONf_chiral_restr0.0742688
X-RAY DIFFRACTIONf_plane_restr0.0073019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0992-2.13540.27253540.24226247X-RAY DIFFRACTION85
2.1354-2.17420.27543750.22946568X-RAY DIFFRACTION89
2.1742-2.2160.26243300.23256368X-RAY DIFFRACTION87
2.216-2.26120.27433140.22136266X-RAY DIFFRACTION84
2.2612-2.31040.25013620.20756623X-RAY DIFFRACTION90
2.3104-2.36410.22913590.20626759X-RAY DIFFRACTION91
2.3641-2.42320.23163600.19936688X-RAY DIFFRACTION91
2.4232-2.48860.21363380.18616734X-RAY DIFFRACTION91
2.4886-2.56180.20173500.18756606X-RAY DIFFRACTION90
2.5618-2.64440.22413390.18766691X-RAY DIFFRACTION90
2.6444-2.73890.20523500.17936556X-RAY DIFFRACTION89
2.7389-2.84840.21333620.17136544X-RAY DIFFRACTION88
2.8484-2.97790.19273260.15836544X-RAY DIFFRACTION88
2.9779-3.13470.18363230.15686355X-RAY DIFFRACTION86
3.1347-3.33070.20483060.1586048X-RAY DIFFRACTION82
3.3307-3.58740.17093490.14596549X-RAY DIFFRACTION88
3.5874-3.94740.16313430.1356483X-RAY DIFFRACTION88
3.9474-4.51640.13483600.1166431X-RAY DIFFRACTION86
4.5164-5.68160.14293460.11926241X-RAY DIFFRACTION83
5.6816-27.17240.18052750.15816184X-RAY DIFFRACTION82
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.09920.92730.27022.7524-0.04592.56890.1316-0.182-0.17890.1061-0.10050.04980.2811-0.0514-0.02660.1553-0.0197-0.01010.17820.01090.169619.6283-80.956465.1212
22.11760.7115-0.20812.7541-0.32672.74280.1688-0.3499-0.08260.4462-0.14590.16250.1464-0.0273-0.0140.2194-0.02630.03880.22140.00280.2027-28.3143-81.515566.0206
32.28470.214-0.29052.1842-0.36681.87270.0488-0.02860.20950.181-0.1094-0.115-0.25360.23710.05020.1796-0.0383-0.02350.21830.00180.138141.5109-54.684-2.9433
42.09020.1735-0.55222.1235-0.15251.16490.023-0.00180.31930.0177-0.00050.0391-0.11560.0151-0.01180.1353-0.0101-0.02210.15970.00740.169-8.6499-54.780545.6741
51.96280.412-0.27642.6144-0.17841.8965-0.0132-0.01280.0633-0.0336-0.0803-0.1274-0.04190.24090.08930.1211-0.0038-0.01610.21530.03710.1848-7.9176-54.5461-1.4101
62.77540.1783-0.53162.837-0.64982.0659-0.0320.14250.2051-0.22280.0331-0.1168-0.05130.01440.00270.1394-0.0205-0.02370.17020.00340.165840.2544-54.838345.4439
70.88270.276-0.46062.42110.12162.23560.006-0.0061-0.1175-0.0464-0.0112-0.04490.1853-0.01390.00340.11930.0026-0.0240.18390.02920.145321.6505-81.40416.8231
81.80030.6689-0.18572.66070.03262.86680.044-0.0617-0.10840.0212-0.08810.03040.3028-0.00540.05150.1598-0.0056-0.01220.17650.00850.1649-27.6968-81.524918.0564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND ((RESSEQ 3:272))
2X-RAY DIFFRACTION2CHAIN B AND ((RESSEQ 3:272))
3X-RAY DIFFRACTION3CHAIN C AND ((RESSEQ 3:272))
4X-RAY DIFFRACTION4CHAIN D AND ((RESSEQ 3:272))
5X-RAY DIFFRACTION5CHAIN E AND ((RESSEQ 3:272))
6X-RAY DIFFRACTION6CHAIN F AND ((RESSEQ 3:272))
7X-RAY DIFFRACTION7CHAIN G AND ((RESSEQ 3:272))
8X-RAY DIFFRACTION8CHAIN H AND ((RESSEQ 3:272))

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