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- PDB-5jtf: Crystal structure of ArsN N-acetyltransferase from Pseudomonas pu... -

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Basic information

Entry
Database: PDB / ID: 5jtf
TitleCrystal structure of ArsN N-acetyltransferase from Pseudomonas putida KT2440
ComponentsPutative Phosphinothricin N-acetyltransferase
KeywordsTRANSFERASE / N-acetyltransferase / Pseudomonas putida
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Acetyltransferase (GNAT) domain / 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
Phosphinothricin N-acetyltransferase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.156 Å
AuthorsVenkadesh, S. / Dheeman, D.S. / Kandavelu, P. / Rosen, B.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37 GM55425 United States
CitationJournal: Commun Biol / Year: 2019
Title: Arsinothricin, an arsenic-containing non-proteinogenic amino acid analog of glutamate, is a broad-spectrum antibiotic.
Authors: Nadar, V.S. / Chen, J. / Dheeman, D.S. / Galvan, A.E. / Yoshinaga-Sakurai, K. / Kandavelu, P. / Sankaran, B. / Kuramata, M. / Ishikawa, S. / Rosen, B.P. / Yoshinaga, M.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 Phosphinothricin N-acetyltransferase
B: Putative Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8853
Polymers46,7632
Non-polymers1221
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-8 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.017, 67.017, 206.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-435-

HOH

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Components

#1: Protein Putative Phosphinothricin N-acetyltransferase


Mass: 23381.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: PP_1924 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88LK7
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium acetate, 0.1 M TRIS HC (pH 8.5), 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.156→30.644 Å / Num. obs: 25849 / % possible obs: 97.76 % / Redundancy: 5.16 % / Rsym value: 0.0784 / Net I/σ(I): 6.88
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 4.31 % / Mean I/σ(I) obs: 2.91 / % possible all: 90.81

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YVO

1yvo


Resolution: 2.156→30.644 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 1310 5.08 %
Rwork0.2377 --
obs0.2391 25795 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.156→30.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 8 95 2774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042759
X-RAY DIFFRACTIONf_angle_d0.9053765
X-RAY DIFFRACTIONf_dihedral_angle_d15.399950
X-RAY DIFFRACTIONf_chiral_restr0.069412
X-RAY DIFFRACTIONf_plane_restr0.004488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1565-2.24280.38721410.34212547X-RAY DIFFRACTION95
2.2428-2.34480.32011430.32222663X-RAY DIFFRACTION98
2.3448-2.46840.35481550.30772668X-RAY DIFFRACTION98
2.4684-2.6230.33091440.26682691X-RAY DIFFRACTION99
2.623-2.82540.31611260.25472714X-RAY DIFFRACTION98
2.8254-3.10950.25021740.22812698X-RAY DIFFRACTION98
3.1095-3.55880.25931310.22192757X-RAY DIFFRACTION98
3.5588-4.48150.23621530.19452778X-RAY DIFFRACTION98
4.4815-30.64670.19161430.19552969X-RAY DIFFRACTION98

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