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- PDB-3d9w: Crystal Structure Analysis of Nocardia farcinica Arylamine N-acet... -

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Basic information

Entry
Database: PDB / ID: 3d9w
TitleCrystal Structure Analysis of Nocardia farcinica Arylamine N-acetyltransferase
ComponentsPutative acetyltransferase
KeywordsTRANSFERASE / ARYLAMINE N-ACETYLTRANSFERASE / NAT / Acyltransferase
Function / homology
Function and homology information


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
Putative acetyltransferase
Similarity search - Component
Biological speciesNocardia farcinica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi de la Sierra-Gallay, I. / Pluvinage, B. / Rodrigues-Lima, F. / Martins, M. / Dupret, J.M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Functional and structural characterization of the arylamine N-acetyltransferase from the opportunistic pathogen Nocardia farcinica
Authors: Martins, M. / Pluvinage, B. / Li de la Sierra-Gallay, I. / Barbault, F. / Dairou, J. / Dupret, J.M. / Rodrigues-Lima, F.
History
DepositionMay 28, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
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: Putative acetyltransferase
B: Putative acetyltransferase
C: Putative acetyltransferase
D: Putative acetyltransferase


Theoretical massNumber of molelcules
Total (without water)131,4644
Polymers131,4644
Non-polymers00
Water4,432246
1
A: Putative acetyltransferase


Theoretical massNumber of molelcules
Total (without water)32,8661
Polymers32,8661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative acetyltransferase


Theoretical massNumber of molelcules
Total (without water)32,8661
Polymers32,8661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative acetyltransferase


Theoretical massNumber of molelcules
Total (without water)32,8661
Polymers32,8661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative acetyltransferase


Theoretical massNumber of molelcules
Total (without water)32,8661
Polymers32,8661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Putative acetyltransferase
B: Putative acetyltransferase


Theoretical massNumber of molelcules
Total (without water)65,7322
Polymers65,7322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-16 kcal/mol
Surface area22560 Å2
MethodPISA
6
C: Putative acetyltransferase
D: Putative acetyltransferase


Theoretical massNumber of molelcules
Total (without water)65,7322
Polymers65,7322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-16 kcal/mol
Surface area22080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.340, 140.920, 74.850
Angle α, β, γ (deg.)90.000, 101.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative acetyltransferase / ARYLAMINE N-ACETYLTRANSFERASE


Mass: 32865.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia farcinica (bacteria) / Strain: IFM 10152 / Gene: nfa18420 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5YYQ3, arylamine N-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG, 0.8M NaCl, 0.1M Bicine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2007
RadiationMonochromator: Diamond (111), Ge(220), Toroidal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 34097 / Num. obs: 33425 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 12.63
Reflection shellResolution: 2.7→3 Å / Redundancy: 5.34 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 3.74 / Num. unique all: 8735 / % possible all: 94.7

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BSZ

2bsz


Resolution: 2.7→45.7 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2574876 / 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
Rfree0.251 1672 5 %RANDOM
Rwork0.19 ---
obs-33425 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.043 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-11.76 Å20 Å2-5.98 Å2
2---7.06 Å20 Å2
3----4.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8984 0 0 246 9230
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it0.961.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it1.462
X-RAY DIFFRACTIONc_scangle_it2.232.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 268 5 %
Rwork0.26 5084 -
all-5352 -
obs--94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3cis_peptide.param

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