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- PDB-6m7g: Crystal structure of ArsN, N-acetyltransferase with substrate pho... -

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Basic information

Entry
Database: PDB / ID: 6m7g
TitleCrystal structure of ArsN, N-acetyltransferase with substrate phosphinothricin 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
PHOSPHINOTHRICIN / Phosphinothricin N-acetyltransferase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.657 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 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
G: Phosphinothricin N-acetyltransferase
H: Phosphinothricin N-acetyltransferase
I: Phosphinothricin N-acetyltransferase
J: Phosphinothricin N-acetyltransferase
K: Phosphinothricin N-acetyltransferase
L: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,02520
Polymers280,57612
Non-polymers1,4498
Water3,981221
1
A: Phosphinothricin N-acetyltransferase
hetero molecules

D: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1254
Polymers46,7632
Non-polymers3622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4180 Å2
ΔGint3 kcal/mol
Surface area14940 Å2
MethodPISA
2
B: Phosphinothricin N-acetyltransferase
C: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1254
Polymers46,7632
Non-polymers3622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint2 kcal/mol
Surface area14950 Å2
MethodPISA
3
E: Phosphinothricin N-acetyltransferase
I: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9443
Polymers46,7632
Non-polymers1811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-4 kcal/mol
Surface area15230 Å2
MethodPISA
4
F: Phosphinothricin N-acetyltransferase
J: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9443
Polymers46,7632
Non-polymers1811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-3 kcal/mol
Surface area15230 Å2
MethodPISA
5
G: Phosphinothricin N-acetyltransferase
L: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9443
Polymers46,7632
Non-polymers1811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-3 kcal/mol
Surface area15230 Å2
MethodPISA
6
H: Phosphinothricin N-acetyltransferase
hetero molecules

K: Phosphinothricin N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)46,9443
Polymers46,7632
Non-polymers1811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area3510 Å2
ΔGint-3 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.841, 142.693, 178.308
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphinothricin N-acetyltransferase


Mass: 23381.311 Da / Num. of mol.: 12
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 BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q88LK7
#2: Chemical
ChemComp-PPQ / PHOSPHINOTHRICIN / 2-AMINO-4-(HYDROXYMETHYL-PHOSPHINYL)BUTANOIC ACID


Mass: 181.127 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H12NO4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1 M Sodium acetate, 1.5 M Sodium formate

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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: Apr 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.657→39.908 Å / Num. obs: 75010 / % possible obs: 97 % / Redundancy: 4.2 % / Rrim(I) all: 0.178 / Net I/σ(I): 11
Reflection shellResolution: 2.657→2.7 Å / Redundancy: 3.9 % / Num. unique obs: 3762 / Rrim(I) all: 1.32 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JTF

5jtf


Resolution: 2.657→39.908 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.26
RfactorNum. reflection% reflection
Rfree0.2726 3550 5.02 %
Rwork0.2243 --
obs0.2267 70774 91.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.657→39.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15829 0 88 221 16138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416317
X-RAY DIFFRACTIONf_angle_d0.8822308
X-RAY DIFFRACTIONf_dihedral_angle_d14.5695540
X-RAY DIFFRACTIONf_chiral_restr0.0622485
X-RAY DIFFRACTIONf_plane_restr0.0042886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6572-2.69350.3312750.29261643X-RAY DIFFRACTION54
2.6935-2.7320.36741110.29672042X-RAY DIFFRACTION72
2.732-2.77280.37721300.27752372X-RAY DIFFRACTION80
2.7728-2.81610.34531250.27812493X-RAY DIFFRACTION85
2.8161-2.86230.3671390.26772590X-RAY DIFFRACTION88
2.8623-2.91160.30561540.26152630X-RAY DIFFRACTION91
2.9116-2.96450.30671510.25362735X-RAY DIFFRACTION93
2.9645-3.02150.27091560.25162767X-RAY DIFFRACTION94
3.0215-3.08320.34151380.27512832X-RAY DIFFRACTION96
3.0832-3.15020.29591440.24422866X-RAY DIFFRACTION97
3.1502-3.22350.3091460.22652851X-RAY DIFFRACTION98
3.2235-3.3040.27471530.22662926X-RAY DIFFRACTION98
3.304-3.39330.29121490.22612862X-RAY DIFFRACTION98
3.3933-3.49310.31621270.24322701X-RAY DIFFRACTION93
3.4931-3.60580.26981350.22612814X-RAY DIFFRACTION94
3.6058-3.73460.30761330.22722517X-RAY DIFFRACTION86
3.7346-3.8840.2781790.22212723X-RAY DIFFRACTION93
3.884-4.06060.24651480.18962738X-RAY DIFFRACTION94
4.0606-4.27440.23181500.18342885X-RAY DIFFRACTION99
4.2744-4.54190.20271450.16822958X-RAY DIFFRACTION99
4.5419-4.8920.21731410.17212939X-RAY DIFFRACTION98
4.892-5.38320.24271640.20952886X-RAY DIFFRACTION98
5.3832-6.15980.27331480.22662893X-RAY DIFFRACTION98
6.1598-7.75130.26591650.26062711X-RAY DIFFRACTION92
7.7513-39.91250.26981440.24842850X-RAY DIFFRACTION95

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