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- PDB-4dmo: Crystal structure of the (BACCR)NAT3 arylamine N-acetyltransferas... -

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Basic information

Entry
Database: PDB / ID: 4dmo
TitleCrystal structure of the (BACCR)NAT3 arylamine N-acetyltransferase from Bacillus cereus reveals a unique Cys-His-Glu catalytic triad
ComponentsN-hydroxyarylamine O-acetyltransferase
KeywordsTRANSFERASE / Acetyltransferase
Function / homology
Function and homology information


N-hydroxyarylamine O-acetyltransferase / N-hydroxyarylamine O-acetyltransferase 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
3-(1-methylpiperidinium-1-yl)propane-1-sulfonate / N-hydroxyarylamine O-acetyltransferase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsKubiak, X. / Li de la Sierra-Gallay, I. / Haouz, A. / Weber, P. / Rodrigues-Lima, F.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural and Biochemical Characterization of an Active Arylamine N-Acetyltransferase Possessing a Non-canonical Cys-His-Glu Catalytic Triad.
Authors: Kubiak, X. / Li de la Sierra-Gallay, I. / Chaffotte, A.F. / Pluvinage, B. / Weber, P. / Haouz, A. / Dupret, J.M. / Rodrigues-Lima, F.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Aug 21, 2013Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-hydroxyarylamine O-acetyltransferase
B: N-hydroxyarylamine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8645
Polymers60,2002
Non-polymers6643
Water2,306128
1
A: N-hydroxyarylamine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3212
Polymers30,1001
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-hydroxyarylamine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5433
Polymers30,1001
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.430, 44.520, 132.970
Angle α, β, γ (deg.)90.00, 103.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein N-hydroxyarylamine O-acetyltransferase


Mass: 30100.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Cellular location: Cytosol / Gene: BC_3483, NAT3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q81AS3, N-hydroxyarylamine O-acetyltransferase
#2: Chemical ChemComp-KH2 / 3-(1-methylpiperidinium-1-yl)propane-1-sulfonate


Mass: 221.317 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H19NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.37 M sodium citrate, 0.28 M NDSB-221, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.984 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2011 / Details: collimating (M1) and toroidal (M2) mirrors
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.14→19.967 Å / Num. obs: 28380 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.392 % / Biso Wilson estimate: 45.83 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 19.07
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 7.25 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 4.28 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RemDAqdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LNB

3lnb


Resolution: 2.14→19.95 Å / Cor.coef. Fo:Fc: 0.9417 / Cor.coef. Fo:Fc free: 0.9062 / SU ML: 0.28 / SU R Cruickshank DPI: 0.593 / σ(F): 1.99 / Phase error: 31.95 / Stereochemistry target values: ML
Details: Additional restraint dictionnary file used through the Gelly module implemented in Buster: protgeo_option_chiralrestraint_from_equilib.dat
RfactorNum. reflection% reflection
Rfree0.2549 1420 5 %
Rwork0.202 --
obs0.2047 28380 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.5601 Å20 Å20.0672 Å2
2---0.292 Å20 Å2
3---0.8521 Å2
Refine analyzeLuzzati coordinate error obs: 0.341 Å
Refinement stepCycle: LAST / Resolution: 2.14→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4064 0 42 128 4234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124192
X-RAY DIFFRACTIONf_angle_d1.2385670
X-RAY DIFFRACTIONf_dihedral_angle_d15.6571547
X-RAY DIFFRACTIONf_chiral_restr0.066633
X-RAY DIFFRACTIONf_plane_restr0.006712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.22030.35291340.31332533X-RAY DIFFRACTION94
2.2203-2.30910.30211400.27882672X-RAY DIFFRACTION100
2.3091-2.4140.31011420.24072683X-RAY DIFFRACTION100
2.414-2.5410.30341420.22892704X-RAY DIFFRACTION100
2.541-2.69990.27431420.22372692X-RAY DIFFRACTION100
2.6999-2.90780.29691410.21952679X-RAY DIFFRACTION100
2.9078-3.19930.25631440.21112730X-RAY DIFFRACTION100
3.1993-3.65980.24041420.18082714X-RAY DIFFRACTION100
3.6598-4.60160.20571440.16422743X-RAY DIFFRACTION100
4.6016-19.95060.23541490.18112810X-RAY DIFFRACTION100

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