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- PDB-4nv7: Crystal Structure of Mesorhizobium Loti Arylamine N-acetyltransfe... -

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Basic information

Entry
Database: PDB / ID: 4nv7
TitleCrystal Structure of Mesorhizobium Loti Arylamine N-acetyltransferase 1 In Complex With CoA
ComponentsArylamine N-acetyltransferase
KeywordsTRANSFERASE / 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
COENZYME A / Arylamine N-acetyltransferase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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 ...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_ncs_dom_lim / 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_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 / _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: Arylamine N-acetyltransferase
B: Arylamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2594
Polymers68,7242
Non-polymers1,5352
Water3,891216
1
A: Arylamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1292
Polymers34,3621
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arylamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1292
Polymers34,3621
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-13 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.500, 114.860, 115.610
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: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 5 - 274 / Label seq-ID: 39 - 308

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: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystallization details: Should be 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: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.02→38.54 Å / Num. obs: 47549 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.095 / Rsym value: 0.103 / Net I/σ(I): 12
Reflection shellResolution: 2.02→2.07 Å / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.693

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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: 2.02→37.18 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.81 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22076 2404 5.1 %RANDOM
Rwork0.19314 ---
obs0.19458 45085 99.86 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.072 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2--2.31 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.02→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 96 216 4535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194426
X-RAY DIFFRACTIONr_bond_other_d0.0030.024204
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9876027
X-RAY DIFFRACTIONr_angle_other_deg0.92239614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7085535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54222.293205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54315681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4111544
X-RAY DIFFRACTIONr_chiral_restr0.0720.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214973
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021077
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_it2.6393.4222149
X-RAY DIFFRACTIONr_mcbond_other2.6383.4192148
X-RAY DIFFRACTIONr_mcangle_it4.0155.1162681
X-RAY DIFFRACTIONr_mcangle_other4.0155.1182682
X-RAY DIFFRACTIONr_scbond_it2.7873.7792277
X-RAY DIFFRACTIONr_scbond_other2.7873.7792278
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4695.5633347
X-RAY DIFFRACTIONr_long_range_B_refined6.40527.7134903
X-RAY DIFFRACTIONr_long_range_B_other6.38827.6274839
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16240 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 173 -
Rwork0.263 3285 -
obs--99.88 %

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