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- PDB-5t7e: Crystal structure of Streptomyces hygroscopicus Bialaphos Resista... -

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Basic information

Entry
Database: PDB / ID: 5t7e
TitleCrystal structure of Streptomyces hygroscopicus Bialaphos Resistance (BAR) protein in complex with Coenzyme A and L-phosphinothricin
ComponentsPhosphinothricin N-acetyltransferase
KeywordsTRANSFERASE / Phosphinothricin-deactivating activity GCN5-Related N-Acetyltransferases
Function / homology
Function and homology information


phosphinothricin acetyltransferase / phosphinothricin N-acetyltransferase activity / response to herbicide / response to antibiotic
Similarity search - Function
Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
COENZYME A / PHOSPHINOTHRICIN / Phosphinothricin N-acetyltransferase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChrist, B. / Weng, J.K.
Funding support United States, Switzerland, 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 Program United States
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
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 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Apr 13, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,53214
Polymers85,1244
Non-polymers4,40710
Water7,963442
1
A: Phosphinothricin N-acetyltransferase
hetero molecules

C: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7667
Polymers42,5622
Non-polymers2,2045
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area6710 Å2
ΔGint2 kcal/mol
Surface area15380 Å2
MethodPISA
2
B: Phosphinothricin N-acetyltransferase
D: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7667
Polymers42,5622
Non-polymers2,2045
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-0 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.180, 66.110, 86.150
Angle α, β, γ (deg.)90.00, 103.06, 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)
References: UniProt: P16426, phosphinothricin acetyltransferase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-PPQ / PHOSPHINOTHRICIN / 2-AMINO-4-(HYDROXYMETHYL-PHOSPHINYL)BUTANOIC ACID


Mass: 181.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12NO4P
#4: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.15 Å3/Da / Density % sol: 42.69 %
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). Several crystals were soaked in reservoir solution supplemented with 30 mM L-phosphinothricin for 30-60 min before freezing. Crystals were frozen in reservoir solution supplemented with 15% (v/v) ethylene glycol. Acetylation of phosphinothricin occurred during soaking as no density for the acetyl group of acetyl-CoA was observed in the BAR/CoA/phosphinothricin ternary complex.

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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: 1.8→62.52 Å / Num. obs: 93996 / % possible obs: 83.62 % / Redundancy: 1.7 % / CC1/2: 0.96 / Net I/σ(I): 5.41

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Processing

Software
NameVersionClassification
PHENIX(dev_2499: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→62.52 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 3382 3.66 %
Rwork0.2084 --
obs0.2098 92528 72.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→62.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 278 442 6262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026008
X-RAY DIFFRACTIONf_angle_d0.598249
X-RAY DIFFRACTIONf_dihedral_angle_d17.8932197
X-RAY DIFFRACTIONf_chiral_restr0.043881
X-RAY DIFFRACTIONf_plane_restr0.0031037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82570.3507600.34271592X-RAY DIFFRACTION31
1.8257-1.8530.3175650.34011669X-RAY DIFFRACTION32
1.853-1.88190.3826650.30971659X-RAY DIFFRACTION32
1.8819-1.91280.3252860.32412146X-RAY DIFFRACTION43
1.9128-1.94580.39881080.33952848X-RAY DIFFRACTION55
1.9458-1.98120.29971080.28822884X-RAY DIFFRACTION57
1.9812-2.01930.24221100.27372830X-RAY DIFFRACTION55
2.0193-2.06050.2887960.26882490X-RAY DIFFRACTION48
2.0605-2.10530.3337940.27982630X-RAY DIFFRACTION52
2.1053-2.15430.35181210.25473160X-RAY DIFFRACTION61
2.1543-2.20810.25851350.23373682X-RAY DIFFRACTION72
2.2081-2.26790.33021610.27974487X-RAY DIFFRACTION87
2.2679-2.33460.29091820.22864754X-RAY DIFFRACTION94
2.3346-2.40990.26891760.21334798X-RAY DIFFRACTION93
2.4099-2.49610.28371700.21644428X-RAY DIFFRACTION86
2.4961-2.5960.23961810.20564675X-RAY DIFFRACTION91
2.596-2.71420.22661820.19974986X-RAY DIFFRACTION96
2.7142-2.85730.21181800.20294858X-RAY DIFFRACTION95
2.8573-3.03630.22111900.20314896X-RAY DIFFRACTION95
3.0363-3.27070.231740.19524550X-RAY DIFFRACTION89
3.2707-3.59980.23661880.17184886X-RAY DIFFRACTION95
3.5998-4.12060.18981830.16684862X-RAY DIFFRACTION95
4.1206-5.19120.21941780.14174579X-RAY DIFFRACTION90
5.1912-62.55760.21111890.2114797X-RAY DIFFRACTION93

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