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- PDB-1e2t: Arylamine N-acetyltransferase (NAT) from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 1e2t
TitleArylamine N-acetyltransferase (NAT) from Salmonella typhimurium
ComponentsN-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
KeywordsTRANSFERASE / ACETYL COA DEPENDENT
Function / homology
Function and homology information


N-hydroxyarylamine O-acetyltransferase / N-hydroxyarylamine O-acetyltransferase activity / arylamine N-acetyltransferase / arylamine N-acetyltransferase activity / cytoplasm
Similarity search - Function
Arylsulfatase, C-terminal domain - #150 / Helix Hairpins - #1930 / Cysteine proteinases / Arylamine N-acetyltransferase / N-acetyltransferase / Arylsulfatase, C-terminal domain / Helix Hairpins / Lipocalin / Helix non-globular / Papain-like cysteine peptidase superfamily ...Arylsulfatase, C-terminal domain - #150 / Helix Hairpins - #1930 / Cysteine proteinases / Arylamine N-acetyltransferase / N-acetyltransferase / Arylsulfatase, C-terminal domain / Helix Hairpins / Lipocalin / Helix non-globular / Papain-like cysteine peptidase superfamily / Special / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Arylamine N-acetyltransferase / N-hydroxyarylamine O-acetyltransferase
Similarity search - Component
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsSinclair, J.C. / Sandy, J. / Delgoda, R. / Sim, E. / Noble, M.E.M.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Structure of Arylamine N-Acetyltransferase Reveals a Catalytic Triad
Authors: Sinclair, J.C. / Sandy, J. / Delgoda, R. / Sim, E. / Noble, M.E.M.
#1: Journal: Protein Expr.Purif. / Year: 1998
Title: Purification, Characterization, and Crystallization of an N-Hydroxyarylamine O-Acetyltransferase from Salmonella Typhimurium
Authors: Sinclair, J.C. / Delgoda, R. / Noble, M.E. / Jarmin, S. / Goh, N.K. / Sim, E.
History
DepositionMay 24, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
B: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
C: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
D: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
E: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
F: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
G: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
H: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)260,0158
Polymers260,0158
Non-polymers00
Water8,431468
1
A: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
B: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
C: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
D: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE

A: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
B: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
C: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
D: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)260,0158
Polymers260,0158
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area15070 Å2
ΔGint-83 kcal/mol
Surface area104140 Å2
MethodPQS
2
E: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
F: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
G: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
H: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE

E: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
F: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
G: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE
H: N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)260,0158
Polymers260,0158
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area15760 Å2
ΔGint-83 kcal/mol
Surface area104210 Å2
MethodPQS
Unit cell
Length a, b, c (Å)134.530, 222.419, 104.662
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.81182, -0.57722, -0.08812), (-0.5685, 0.74689, 0.34492), (-0.13327, 0.33011, -0.93449)223.10291, 50.76181, 115.83584
2given(-0.46048, -0.00013, 0.88767), (0.0267, -0.99955, 0.0137), (0.88727, 0.03001, 0.46027)74.20797, 168.87569, -47.90586
3given(0.29006, 0.56335, -0.77363), (0.56105, -0.75499, -0.33942), (-0.77529, -0.3356, -0.53507)69.67397, 122.64743, 205.04736
4given(-0.99759, 0.06832, -0.01229), (0.0684, 0.99764, -0.00622), (0.01183, -0.00704, -0.99991)127.68368, -3.58313, 84.94181
5given(0.76867, 0.62681, 0.12753), (-0.62811, 0.70194, 0.3358), (0.12096, -0.33822, 0.93326)-93.19045, 62.69694, -28.65072
6given(-0.20881, -0.61084, 0.76372), (0.5946, -0.69931, -0.39676), (0.77644, 0.37126, 0.50922)60.31319, 120.53935, -121.20006
7given(0.44425, -0.07801, -0.8925), (0.00719, -0.99586, 0.09063), (-0.89587, -0.04668, -0.44185)67.10536, 167.01891, 134.24864

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Components

#1: Protein
N-HYDROXYARYLAMINE O-ACETYLTRANSFERASE / NAT


Mass: 32501.852 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Gene: NHOA / Plasmid: PET-28B / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q00267, N-hydroxyarylamine O-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growpH: 6.8 / Details: pH 6.80
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.9 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1drop
3100 mM1dropNaCl
43 mMdithiothreitol1drop
50.8 MNa/K tartrate1reservoir
60.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933, 0.979
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
20.9791
ReflectionResolution: 2.8→50 Å / Num. obs: 73897 / % possible obs: 94.7 % / Redundancy: 3.2 % / Rsym value: 0.059 / Net I/σ(I): 8.3
Reflection
*PLUS
Num. measured all: 235995 / Rmerge(I) obs: 0.059

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Processing

Software
NameVersionClassification
CNS0.5refinement
MOSFLMdata reduction
SCALEPACKdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE LAST 8 RESIDUES WERE NOT SEEN IN THE DENSITY MAPS IN CHAIN A, B, C, D, E, F, G, H
RfactorNum. reflection% reflection
Rfree0.302 -5 %
Rwork0.264 --
obs0.264 72898 94.7 %
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17792 0 0 468 18260
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.81
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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