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- PDB-2o0x: Mycobacterium tuberculosis epsp synthase in complex with intermediate -

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Basic information

Entry
Database: PDB / ID: 2o0x
TitleMycobacterium tuberculosis epsp synthase in complex with intermediate
Components3-phosphoshikimate 1-carboxyvinyltransferase
KeywordsTRANSFERASE / SHIKIMATE PATHWAY / EPSP SYNTHASE / M.TUBERCULOSIS / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB
Function / homology
Function and homology information


3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / plasma membrane / cytoplasm / cytosol
Similarity search - Function
EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) ...EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Alpha Beta
Similarity search - Domain/homology
Chem-SKP / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.96 Å
AuthorsKachalova, G.S. / Bartunik, H.D. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: To be Published
Title: Complexes of 3-PHOSPHOSHIKIMATE 1-CARBOXYVINYLTRANSFERASE
Authors: Kachalova, G.S. / Burenkov, G.P. / Strizhov, N.I. / Brunning, M.G. / Bartunik, H.D.
History
DepositionNov 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0884
Polymers46,4741
Non-polymers6143
Water11,926662
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.729, 73.104, 128.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-phosphoshikimate 1-carboxyvinyltransferase / 5-enolpyruvylshikimate-3-phosphate synthase / EPSP synthase / EPSPS


Mass: 46473.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: aroA / Plasmid: p7b, pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: P22487, UniProt: P9WPY5*PLUS, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SKP / 5-(1-CARBOXY-1-PHOSPHONOOXY-ETHOXYL)-4-HYDROXY-3-PHOSPHONOOXY-CYCLOHEX-1-ENECARBOXYLIC ACID / 5-(1-CARBOXY-1-PHOSPHONOOXY-ETHOXYL)-SHIKIMATE-3-PHOSPHATE


Mass: 422.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / 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: 1.86 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2M Ammonium sulfate ; 30%PEG 6000; 5mM S3P, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 25, 2004 / Details: Au-coated planar; toroidal mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 28183 / Num. obs: 27055 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 13
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / Num. unique all: 1104 / % possible all: 89

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2O0D

2o0d


Resolution: 1.96→10 Å / Num. parameters: 15858 / Num. restraintsaints: 14301 / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
Rwork0.119 --
all0.1481 26807 -
obs-25493 95.1 %
Displacement parametersBiso mean: 23.9 Å2
Refine analyzeNum. disordered residues: 63 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3698.8
Refinement stepCycle: LAST / Resolution: 1.96→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 36 680 4000
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0.003
X-RAY DIFFRACTIONs_from_restr_planes0.0253
X-RAY DIFFRACTIONs_zero_chiral_vol0.032
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.083
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.96→1.98 Å
RfactorNum. reflection% reflection
Rwork0.192 --
obs-729 82 %

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