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- PDB-2bsz: Structure of Mesorhizobium loti arylamine N-acetyltransferase 1 -

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Basic information

Entry
Database: PDB / ID: 2bsz
TitleStructure of Mesorhizobium loti arylamine N-acetyltransferase 1
ComponentsARYLAMINE N-ACETYLTRANSFERASE 1
KeywordsTRANSFERASE / ACYLTRANSFERASE
Function / homology
Function and homology information


arylamine N-acetyltransferase / arylamine N-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
Similarity search - Component
Biological speciesRHIZOBIUM LOTI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHolton, S.J. / Dairou, J. / Sandy, J. / Rodrigues-Lima, F. / Dupret, J.-M. / Noble, M.E.M. / Sim, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Structure of Mesorhizobium Loti Arylamine N-Acetyltransferase 1.
Authors: Holton, S.J. / Dairou, J. / Sandy, J. / Rodrigues-Lima, F. / Dupret, J.M. / Noble, M.E.M. / Sim, E.
History
DepositionMay 24, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2005Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 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:
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Assembly

Deposited unit
A: ARYLAMINE N-ACETYLTRANSFERASE 1
B: ARYLAMINE N-ACETYLTRANSFERASE 1


Theoretical massNumber of molelcules
Total (without water)61,5742
Polymers61,5742
Non-polymers00
Water4,612256
1
A: ARYLAMINE N-ACETYLTRANSFERASE 1


Theoretical massNumber of molelcules
Total (without water)30,7871
Polymers30,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ARYLAMINE N-ACETYLTRANSFERASE 1


Theoretical massNumber of molelcules
Total (without water)30,7871
Polymers30,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.239, 97.304, 114.346
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ARYLAMINE N-ACETYLTRANSFERASE 1


Mass: 30786.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHIZOBIUM LOTI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q98D42, arylamine N-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.39 Å3/Da / Density % sol: 48.08 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→25.08 Å / Num. obs: 40315 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.85
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.25 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GX3

1gx3


Resolution: 2→74.54 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2025 5 %RANDOM
Rwork0.195 ---
obs0.198 38238 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2--2.63 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4174 0 0 256 4430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214271
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9565798
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2275527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023294
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21844
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2300
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9951.52636
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83724216
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.71631635
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4854.51582
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
Rfree0.284 132
Rwork0.247 2507

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