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- PDB-2j8n: Structure of P. aeruginosa acetyltransferase PA4866 solved at roo... -

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Basic information

Entry
Database: PDB / ID: 2j8n
TitleStructure of P. aeruginosa acetyltransferase PA4866 solved at room temperature
ComponentsACETYLTRANSFERASE PA4866 FROM P. AERUGINOSA
KeywordsTRANSFERASE / GCN5 FAMILY / PHOSPHINOTHRICIN / METHIONINE SULFONE / PSEUDOMONAS AERUGINOSA / METHIONINE SULFOXIMINE / N-ACETYL TRANSFERASE / HYPOTHETICAL PROTEIN
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-methionine sulfoximine/L-methionine sulfone acetyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDavies, A.M. / Tata, R. / Beavil, R.L. / Sutton, B.J. / Brown, P.R.
Citation
Journal: Biochemistry / Year: 2007
Title: l-Methionine sulfoximine, but not phosphinothricin, is a substrate for an acetyltransferase (gene PA4866) from Pseudomonas aeruginosa: structural and functional studies.
Authors: Davies, A.M. / Tata, R. / Beavil, R.L. / Sutton, B.J. / Brown, P.R.
#1: Journal: Proteins: Struct.,Funct., Genet. / Year: 2005
Title: Crystal Structure of a Putative Phosphinothricin Acetyltransferase (Pa4866) from Pseudomonas Aeruginosa Pac1
Authors: Davies, A.M. / Tata, R. / Agha, R. / Sutton, B.J. / Brown, P.R.
History
DepositionOct 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 6, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / citation_author / exptl_crystal_grow
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5Jun 12, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Dec 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYLTRANSFERASE PA4866 FROM P. AERUGINOSA
B: ACETYLTRANSFERASE PA4866 FROM P. AERUGINOSA


Theoretical massNumber of molelcules
Total (without water)37,4642
Polymers37,4642
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.967, 57.522, 126.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.85411, 0.5099, 0.10244), (0.50735, 0.77356, 0.37973), (0.11438, 0.37631, -0.91941)
Vector: 6.54262, -22.71957, 97.6962)

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Components

#1: Protein ACETYLTRANSFERASE PA4866 FROM P. AERUGINOSA


Mass: 18732.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAC1 (8602) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HUU7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN STRAIN PAC1, RESIDUE 47 IS ALA, AS OPPOSED TO THR IN STRAIN PAO1, SEQUENCE DISCREPANCY BETWEEN ...IN STRAIN PAC1, RESIDUE 47 IS ALA, AS OPPOSED TO THR IN STRAIN PAO1, SEQUENCE DISCREPANCY BETWEEN PAC1 AND PAO1.

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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: 2.43 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOR DIFFUSION. RESERVOIR SOLUTION CONTAINED 100MM SODIUM CACODYLATE AT PH 6.5 OR 100MM TRIS-HCL AT PH7.5, 18-22% (W/V) PEG 10 000 AND 0.1% (W/V) NAN3. PROTEIN CONCENTRATION OF ...Details: HANGING DROP VAPOR DIFFUSION. RESERVOIR SOLUTION CONTAINED 100MM SODIUM CACODYLATE AT PH 6.5 OR 100MM TRIS-HCL AT PH7.5, 18-22% (W/V) PEG 10 000 AND 0.1% (W/V) NAN3. PROTEIN CONCENTRATION OF 10 MG/ML. DROPS KEPT AT 291K.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 29, 2002 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.35→60 Å / Num. obs: 14726 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.7
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.8 / % possible all: 97.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J8M

2j8m


Resolution: 2.35→6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 718 0.07 %RANDOM
Rwork0.1888 ---
obs0.1888 14726 97.2 %-
Solvent computationBsol: 28.15 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.25 Å
Luzzati d res low-6 Å
Luzzati sigma a0.23 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.35→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 0 180 2789
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.12
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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