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- PDB-2jdd: Glyphosate N-acetyltransferase bound to acetyl COA and 3-phosphog... -

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Basic information

Entry
Database: PDB / ID: 2jdd
TitleGlyphosate N-acetyltransferase bound to acetyl COA and 3-phosphoglycerate
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
3-PHOSPHOGLYCERIC ACID / ACETYL 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 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 19, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / pdbx_struct_special_symmetry / struct_conn
Item: _atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id ..._atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYPHOSATE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7174
Polymers16,6251
Non-polymers1,0923
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.828, 48.448, 46.798
Angle α, β, γ (deg.)90.00, 103.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

21A-2011-

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-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 129 / 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 ...THE N-TERMINAL METHIONINE RESIDUE IS DISORDERED IN THE ELECTRON DENSITY, AND WAS NOT MODELED. THE SEQUENCE HAS ACCESSION NUMBER AY597417 IN GENBANK DATABASE

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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 20 MM D-3-PHOSPHOGLYCERATE

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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→45.6 Å / Num. obs: 19905 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 41.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 8.3 / % possible all: 89.6

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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→45.64 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.643 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A MINOR ACTIVE SITE CONFIGURATION IN WHICH 3PG IS REPLACED BY SO4 AND A WATER MOLECULE WAS MODELED AT 0.3 OCCUPANCY. DISORDERED OR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A MINOR ACTIVE SITE CONFIGURATION IN WHICH 3PG IS REPLACED BY SO4 AND A WATER MOLECULE WAS MODELED AT 0.3 OCCUPANCY. DISORDERED OR RADIATION DAMAGED SURFACE SIDECHAIN ATOMS WERE MODELED AT 0.5 OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1014 5.1 %RANDOM
Rwork0.155 ---
obs0.157 18899 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.11 Å2
2---0.09 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 67 129 1357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211273
X-RAY DIFFRACTIONr_bond_other_d0.0020.021133
X-RAY DIFFRACTIONr_angle_refined_deg1.4482.0271725
X-RAY DIFFRACTIONr_angle_other_deg0.77632636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0495150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.38722.88159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47615219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7741511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021386
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02269
X-RAY DIFFRACTIONr_nbd_refined0.1990.2216
X-RAY DIFFRACTIONr_nbd_other0.1980.21134
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2599
X-RAY DIFFRACTIONr_nbtor_other0.0830.2704
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0550.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3741.5945
X-RAY DIFFRACTIONr_mcbond_other0.4011.5303
X-RAY DIFFRACTIONr_mcangle_it1.6121163
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3973635
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0784.5559
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.28932922
X-RAY DIFFRACTIONr_sphericity_free5.5773129
X-RAY DIFFRACTIONr_sphericity_bonded2.02332377
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.161 84 -
Rwork0.116 1237 -
obs--100 %

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