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- PDB-5t7d: Crystal structure of Streptomyces hygroscopicus bialaphos resista... -

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Basic information

Entry
Database: PDB / ID: 5t7d
TitleCrystal structure of Streptomyces hygroscopicus bialaphos resistance (BAR) protein in complex with acetyl coenzyme A
ComponentsPhosphinothricin N-acetyltransferase
KeywordsTRANSFERASE / Gcn5-related N-acetyltransferases Phosphinothricin-deactivating activity
Function / homology
Function and homology information


phosphinothricin acetyltransferase / phosphinothricin N-acetyltransferase activity / response to herbicide / response to antibiotic
Similarity search - Function
Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / ACETATE ION / Phosphinothricin N-acetyltransferase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChrist, B. / Weng, J.K.
Funding support United States, Switzerland, United Arab Emirates, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR029205 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Swiss National Science FoundationP2ZHP3_155258 Switzerland
Pew Scholar Program in the Biomedical Sciences United States
Searle Scholars ProgramUnited Arab Emirates
CitationJournal: Nat Plants / Year: 2017
Title: Non-specific activities of the major herbicide-resistance gene BAR.
Authors: Christ, B. / Hochstrasser, R. / Guyer, L. / Francisco, R. / Aubry, S. / Hortensteiner, S. / Weng, J.K.
History
DepositionSep 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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_author.name
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,83516
Polymers85,1244
Non-polymers3,71112
Water19,3301073
1
A: Phosphinothricin N-acetyltransferase
hetero molecules

C: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4178
Polymers42,5622
Non-polymers1,8556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area6650 Å2
ΔGint-23 kcal/mol
Surface area15510 Å2
MethodPISA
2
B: Phosphinothricin N-acetyltransferase
D: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4178
Polymers42,5622
Non-polymers1,8556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-23 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.100, 71.500, 84.050
Angle α, β, γ (deg.)90.00, 104.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphinothricin N-acetyltransferase / PPT N-acetyltransferase / Phosphinothricin-resistance protein


Mass: 21281.051 Da / Num. of mol.: 4 / Fragment: UNP residues 7-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: bar / Plasmid: pProExHta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P16426, phosphinothricin acetyltransferase
#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C23H38N7O17P3S
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1073 / 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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: BAR protein was incubated with 1 mM acetyl-CoA for >2 hour prior to setting crystal trays. Crystals of BAR were obtained after 3 days at 20C in hanging drops containing 1 uL of protein ...Details: BAR protein was incubated with 1 mM acetyl-CoA for >2 hour prior to setting crystal trays. Crystals of BAR were obtained after 3 days at 20C in hanging drops containing 1 uL of protein solution (7.5 mg/mL) and 1 uL of reservoir solution (0.18 M calcium acetate, 0.1 M Tris-HCl pH 7, 18% (w/v) PEG 3000, 0.2% (v/v) N-nonyl Beta-D-glucopyranoside, 1 mM acetyl-CoA). Crystals were frozen in reservoir solution supplemented with 15% (v/v) ethylene glycol.

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.4→44.79 Å / Num. obs: 238978 / % possible obs: 89.48 % / Redundancy: 1.8 % / Biso Wilson estimate: 14.16 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.84

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Processing

Software
NameVersionClassification
PHENIX(dev_2499: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→44.788 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.69 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1915 3592 1.52 %
Rwork0.1519 --
obs0.1525 236084 81.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→44.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5514 0 236 1073 6823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086094
X-RAY DIFFRACTIONf_angle_d1.1418379
X-RAY DIFFRACTIONf_dihedral_angle_d17.4942171
X-RAY DIFFRACTIONf_chiral_restr0.068874
X-RAY DIFFRACTIONf_plane_restr0.0051080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41840.3861820.33444945X-RAY DIFFRACTION45
1.4184-1.43790.3329770.30954915X-RAY DIFFRACTION45
1.4379-1.45840.3324800.29914858X-RAY DIFFRACTION44
1.4584-1.48020.3336760.294928X-RAY DIFFRACTION45
1.4802-1.50330.3505690.25834606X-RAY DIFFRACTION42
1.5033-1.5280.3472720.2474376X-RAY DIFFRACTION40
1.528-1.55430.2792790.23235273X-RAY DIFFRACTION48
1.5543-1.58260.27331510.229901X-RAY DIFFRACTION91
1.5826-1.6130.23791590.20810176X-RAY DIFFRACTION93
1.613-1.64590.24921620.190110684X-RAY DIFFRACTION97
1.6459-1.68170.23151660.182310484X-RAY DIFFRACTION97
1.6817-1.72080.23591630.164610605X-RAY DIFFRACTION96
1.7208-1.76390.20281610.162510335X-RAY DIFFRACTION95
1.7639-1.81160.18661530.15379886X-RAY DIFFRACTION90
1.8116-1.86490.20471600.150110406X-RAY DIFFRACTION95
1.8649-1.92510.19031680.144910748X-RAY DIFFRACTION98
1.9251-1.99390.19451620.140210721X-RAY DIFFRACTION98
1.9939-2.07370.20321640.128110663X-RAY DIFFRACTION97
2.0737-2.16810.16091650.126310534X-RAY DIFFRACTION96
2.1681-2.28240.15391550.128710102X-RAY DIFFRACTION92
2.2824-2.42540.20851540.13510461X-RAY DIFFRACTION95
2.4254-2.61260.15891690.140610820X-RAY DIFFRACTION99
2.6126-2.87550.17691640.13910637X-RAY DIFFRACTION98
2.8755-3.29150.15311590.144110231X-RAY DIFFRACTION93
3.2915-4.14650.16711640.130810635X-RAY DIFFRACTION97
4.1465-44.81050.18351580.152810562X-RAY DIFFRACTION96

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