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- PDB-3lnb: Crystal Structure Analysis of Arylamine N-acetyltransferase C fro... -

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Basic information

Entry
Database: PDB / ID: 3lnb
TitleCrystal Structure Analysis of Arylamine N-acetyltransferase C from Bacillus anthracis
ComponentsN-acetyltransferase family protein
KeywordsTRANSFERASE / arylamine N-acetyltransferase / nat / acetyltransferase / Acyltransferase
Function / homology
Function and homology information


acetyltransferase activity / transferase activity
Similarity search - Function
Arylamine N-acetyltransferase fold - #20 / Arylamine N-acetyltransferase fold / Arylamine N-acetyltransferase / N-acetyltransferase / Papain-like cysteine peptidase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / FORMIC ACID / Arylamine N-acetyltransferase / N-acetyltransferase family protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsLi de la Sierra-Gallay, I. / Pluvinage, B. / Rodrigues-Lima, F.
CitationJournal: Febs Lett. / Year: 2011
Title: The Bacillus anthracis arylamine N-acetyltransferase ((BACAN)NAT1) that inactivates sulfamethoxazole, reveals unusual structural features compared with the other NAT isoenzymes.
Authors: Pluvinage, B. / Li de la Sierra-Gallay, I. / Kubiak, X. / Xu, X. / Dairou, J. / Dupret, J.M. / Rodrigues-Lima, F.
History
DepositionFeb 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 3, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 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: N-acetyltransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1624
Polymers35,3021
Non-polymers8603
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.990, 53.990, 172.440
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 N-acetyltransferase family protein / arylamine N-acetyltransferase


Mass: 35302.488 Da / Num. of mol.: 1 / Mutation: Y38F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Strain Sterne (RTC50) / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: Q81R98, UniProt: A0A6L7HKL6*PLUS, arylamine N-acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.779778 Å3/Da / Density % sol: 30.890238 %
Crystal growTemperature: 294 K / Method: vapor diffusion
Details: 1.8-1.9M Ammonium sulfate, 0.17M-0.2M potassium nitrate, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2008 / Details: mirrors
RadiationMonochromator: Silicon 1 1 1 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 18116 / Num. obs: 17034 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.68 % / Biso Wilson estimate: 24.85 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.063 / Net I/σ(I): 20.45
Reflection shellResolution: 2→2.2 Å / Redundancy: 4.24 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 7.91 / Num. unique all: 4366 / Rsym value: 0.177 / % possible all: 75.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.69 / Packing: 0.682
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation4 Å15 Åfast direct97.1 0
Translation4 Å15 Ågeneral97.1 0

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
CNS1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E2T

1e2t


Resolution: 2.01→45.76 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2205494 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 852 5 %RANDOM
Rwork0.203 ---
all-18116 --
obs-17034 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.02 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 44.33 Å2 / Biso mean: 19.19 Å2 / Biso min: 8.73 Å2
Baniso -1Baniso -2Baniso -3
1--4.5 Å20 Å20 Å2
2---4.5 Å20 Å2
3---9.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.01→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 54 137 2246
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.62
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.562.5
LS refinement shellResolution: 2.01→2.13 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.226 104 5 %
Rwork0.2 1981 -
all-2085 -
obs--70.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ligands.paramligands.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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