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- PDB-2bsw: Crystal structure of a glyphosate-N-acetyltransferase obtained by... -

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Basic information

Entry
Database: PDB / ID: 2bsw
TitleCrystal structure of a glyphosate-N-acetyltransferase obtained by DNA shuffling.
ComponentsGLYPHOSATE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE / GNAT SUPERFAMILY / 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 speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.63 Å
AuthorsKeenan, R.J. / Siehl, D.L. / Gorton, R. / Castle, L.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: DNA Shuffling as a Tool for Protein Crystallization.
Authors: Keenan, R.J. / Siehl, D.L. / Gorton, R. / Castle, L.A.
History
DepositionMay 24, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: GLYPHOSATE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8765
Polymers16,8131
Non-polymers1,0644
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.323, 49.393, 46.492
Angle α, β, γ (deg.)90.00, 103.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2013-

HOH

21A-2030-

HOH

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Components

#1: Protein GLYPHOSATE N-ACETYLTRANSFERASE


Mass: 16812.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others)
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 46.57 %
Crystal growpH: 4.6
Details: 100 MM SODIUM ACETATE, PH 4.6 250 MM AMMONIUM SULFATE 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97942
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 18939 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 2.94 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.2
Reflection shellResolution: 1.63→1.69 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 8 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.63→45.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.774 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE N-TERMINAL SELENOMETHIONINE, MSE A1, IS DISORDERED IN ELECTRON DENSITY MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 955 5 %RANDOM
Rwork0.179 ---
obs0.181 17983 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.18 Å2
2--0.88 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.63→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 66 161 1388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211307
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.362.0191766
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0025154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.82123.11561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28715223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0941511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02983
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.2541
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2860
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8831.5783
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36421205
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1073602
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8774.5561
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: 1.63→1.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 73
Rwork0.207 1289

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