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- PDB-2jdc: Glyphosate N-acetyltransferase bound to oxidized COA and sulfate -

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Basic information

Entry
Database: PDB / ID: 2jdc
TitleGlyphosate N-acetyltransferase bound to oxidized COA and sulfate
ComponentsGLYPHOSATE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE / GNAT / GLYPHOSATE / N-ACETYLTRANSFERASE
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Acetyltransferase (GNAT) family / 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
OXIDIZED COENZYME A / Probable acetyltransferase
Similarity search - Component
Biological speciesBACILLUS LICHENIFORMIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsSiehl, D.L. / Castle, L.A. / Gorton, R. / Keenan, R.J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Molecular Basis of Glyphosate Resistance by an Optimized Microbial Acetyltransferase.
Authors: Siehl, D.L. / Castle, L.A. / Gorton, R. / Keenan, R.J.
History
DepositionJan 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYPHOSATE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5053
Polymers16,6251
Non-polymers8802
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.056, 48.911, 46.461
Angle α, β, γ (deg.)90.00, 103.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

21A-2017-

HOH

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Components

#1: Protein GLYPHOSATE N-ACETYLTRANSFERASE


Mass: 16624.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS LICHENIFORMIS (bacteria)
Description: THE ENZYME IS A SHUFFLED VARIANT DERIVED FROM GENES DISCOVERED IN B. LICHENIFORMIS.
Plasmid: PQE80 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG1 / References: UniProt: Q65LG7*PLUS
#2: Chemical ChemComp-CAO / OXIDIZED COENZYME A


Mass: 783.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O17P3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL METHIONINE RESIDUE IS DISORDERED IN THE ELECTRON DENSITY, AND WAS NOT MODELED. ...THE N-TERMINAL METHIONINE RESIDUE IS DISORDERED IN THE ELECTRON DENSITY, AND WAS NOT MODELED. SEQUENCE DATABASE: GENBANK DATABASE ACCESSION NUMBER: AY597417

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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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 4.6
Details: 100 MM SODIUM ACETATE, PH 4.6 150-300 MM AMMONIUM SULFATE 20-25% PEG4000 2 MM ACETYL COA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0072
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 4, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0072 Å / Relative weight: 1
ReflectionResolution: 1.6→32.2 Å / Num. obs: 19217 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 47.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 19 / % possible all: 75.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2BSW

2bsw


Resolution: 1.6→32.16 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.568 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PARTIALLY DISORDERED SURFACE SIDECHAINS WERE MODELED STEREOCHEMICALLY. DISORDERED OR RADIATION DAMAGED SURFACE SIDECHAIN ATOMS WERE MODELED AT 0.5 OCCUPANCY
RfactorNum. reflection% reflectionSelection details
Rfree0.172 989 5.19 %RANDOM
Rwork0.148 ---
obs0.149 18217 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.009 Å2
2---0.017 Å20 Å2
3----0.009 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 54 131 1346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211246
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4492.0161685
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1925146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.76523.10358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38615214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9711510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021359
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.2210
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2580
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.090.25
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4081.5936
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59221148
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4913619
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1934.5536
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.194 62
Rwork0.116 999

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