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- PDB-5wph: Crystal structure of ArsN, N-acetyltransferase with substrate AST... -

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Basic information

Entry
Database: PDB / ID: 5wph
TitleCrystal structure of ArsN, N-acetyltransferase with substrate AST from Pseudomonas putida KT2440
ComponentsPhosphinothricin 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
Chem-BLJ / Phosphinothricin N-acetyltransferase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsVenkadesh, S. / Dheeman, D.S. / Yoshinaga, M. / Kandavelu, P. / Rosen, B.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)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
DepositionAug 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Phosphinothricin N-acetyltransferase
B: Phosphinothricin N-acetyltransferase
C: Phosphinothricin N-acetyltransferase
D: Phosphinothricin N-acetyltransferase
E: Phosphinothricin N-acetyltransferase
F: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,83012
Polymers140,2886
Non-polymers5426
Water15,763875
1
A: Phosphinothricin N-acetyltransferase
B: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2596
Polymers46,7632
Non-polymers4964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-35 kcal/mol
Surface area16500 Å2
MethodPISA
2
C: Phosphinothricin N-acetyltransferase
F: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7863
Polymers46,7632
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-23 kcal/mol
Surface area16250 Å2
MethodPISA
3
D: Phosphinothricin N-acetyltransferase
E: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7863
Polymers46,7632
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-23 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.273, 141.735, 54.551
Angle α, β, γ (deg.)90.00, 90.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-522-

HOH

21A-535-

HOH

31B-524-

HOH

41E-387-

HOH

51F-428-

HOH

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Components

#1: Protein
Phosphinothricin N-acetyltransferase


Mass: 23381.311 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: PP_1924 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88LK7
#2: Chemical ChemComp-BLJ / (2S)-2-amino-4-[hydroxy(methyl)arsoryl]butanoic acid


Mass: 225.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12AsNO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / 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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 1.5 M Na formate, 0.1 M Na acetate

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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: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 72209 / % possible obs: 99.4 % / Redundancy: 7.3 % / Rpim(I) all: 0.059 / Rrim(I) all: 0.161 / Net I/σ(I): 12
Reflection shellResolution: 2.19→2.23 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3416 / Rpim(I) all: 0.335 / Rrim(I) all: 0.739 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JTF

5jtf


Resolution: 2.19→49.02 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.132 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.193
RfactorNum. reflection% reflectionSelection details
Rfree0.23225 3600 5.1 %RANDOM
Rwork0.17991 ---
obs0.18257 67549 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.029 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.19→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8390 0 26 875 9291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198690
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.94611844
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97851074
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4621.818418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.133151277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5281593
X-RAY DIFFRACTIONr_chiral_restr0.1170.21275
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216843
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.183→2.239 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 230 -
Rwork0.226 4022 -
obs--79.63 %

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