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- PDB-4nv8: Crystal Structure of Mesorhizobium Loti Arylamine N-acetyltransfe... -

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Basic information

Entry
Database: PDB / ID: 4nv8
TitleCrystal Structure of Mesorhizobium Loti Arylamine N-acetyltransferase F42W Mutant
ComponentsArylamine N-acetyltransferase
KeywordsTRANSFERASE / NAT / Arylamine N-acetyltransferase / acetyltransferase
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 speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsXu, X.M. / Haouz, A. / Weber, P. / Li de la sierra-gallay, I. / Kubiak, X. / Dupret, J.-M. / Rodrigues-lima, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Insight into cofactor recognition in arylamine N-acetyltransferase enzymes: structure of Mesorhizobium loti arylamine N-acetyltransferase in complex with coenzyme A.
Authors: Xu, X. / Li de la Sierra-Gallay, I. / Kubiak, X. / Duval, R. / Chaffotte, A.F. / Dupret, J.M. / Haouz, A. / Rodrigues-Lima, F.
History
DepositionDec 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 20, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arylamine N-acetyltransferase
B: Arylamine N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)68,7242
Polymers68,7242
Non-polymers00
Water3,909217
1
A: Arylamine N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)34,3621
Polymers34,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arylamine N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)34,3621
Polymers34,3621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-8 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.860, 115.080, 115.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 5 - 275 / Label seq-ID: 39 - 309

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Arylamine N-acetyltransferase


Mass: 34361.777 Da / Num. of mol.: 2 / Mutation: F42W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: mlr4870 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q98D42, arylamine N-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 5000, 0.2M ammonium sulfate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07169 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07169 Å / Relative weight: 1
ReflectionResolution: 1.84→32.01 Å / Num. obs: 61856 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Rmerge(I) obs: 0.064 / Rsym value: 0.071 / Net I/σ(I): 14.1
Reflection shellResolution: 1.84→1.89 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.682 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
xia2data reduction
XDSdata reduction
xia2data scaling
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BSZ

2bsz


Resolution: 1.84→32.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.886 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22807 3126 5.1 %RANDOM
Rwork0.2036 ---
obs0.20486 58644 99.61 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.561 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2--2.29 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.84→32.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4224 0 0 217 4441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194335
X-RAY DIFFRACTIONr_bond_other_d0.0050.024158
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9625888
X-RAY DIFFRACTIONr_angle_other_deg1.0639506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25122.233206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24315685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.421545
X-RAY DIFFRACTIONr_chiral_restr0.0880.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214922
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021059
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5723.1472150
X-RAY DIFFRACTIONr_mcbond_other2.5723.1452149
X-RAY DIFFRACTIONr_mcangle_it3.7354.72681
X-RAY DIFFRACTIONr_mcangle_other3.7354.7032682
X-RAY DIFFRACTIONr_scbond_it2.9173.5022185
X-RAY DIFFRACTIONr_scbond_other2.9143.4982183
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5455.1253206
X-RAY DIFFRACTIONr_long_range_B_refined6.35225.5094860
X-RAY DIFFRACTIONr_long_range_B_other6.31625.4234811
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16250 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 231 -
Rwork0.281 4277 -
obs--99.36 %

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