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- PDB-2o0b: Mycobacterium tuberculosis epsp synthase in complex with S3P (par... -

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Basic information

Entry
Database: PDB / ID: 2o0b
TitleMycobacterium tuberculosis epsp synthase in complex with S3P (partially photolyzed)
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 / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / plasma membrane ...3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / Chorismate via Shikimate Pathway / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase activity / 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
PHOSPHATE ION / SHIKIMATE-3-PHOSPHATE / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsBurenkov, G.P. / Kachalova, G.S. / Bartunik, H.D. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: To be Published
Title: Complex of 3-PHOSPHOSHIKIMATE 1-CARBOXYVINYLTRANSFERASE with S3P
Authors: Kachalova, G.S. / Burenkov, G.P. / Strizhov, N.I. / Brunning, M.G. / Bartunik, H.D.
History
DepositionNov 27, 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 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)47,1116
Polymers46,4741
Non-polymers6375
Water10,917606
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.592, 72.794, 127.679
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: pET24b, p7b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: P22487, UniProt: P9WPY5*PLUS, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-S3P / SHIKIMATE-3-PHOSPHATE


Mass: 254.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 2.03 Å3/Da / Density % sol: 39.35 %
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 8, 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: 1.15→15 Å / Num. all: 135040 / Num. obs: 133042 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 19
Reflection shellResolution: 1.15→1.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2 / Num. unique all: 5362 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1g6lt

Resolution: 1.15→10.89 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.901 / SU ML: 0.021 / Isotropic thermal model: mixed anisotropic + isotropic / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15352 6661 5 %RANDOM
Rwork0.12708 ---
all0.1271 129100 --
obs0.12843 126181 97.77 %-
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: 11.287 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.07 Å20 Å2
3---0.13 Å2
Refine analyzeLuzzati coordinate error obs: 0.0304 Å
Refinement stepCycle: LAST / Resolution: 1.15→10.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 36 622 3959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223398
X-RAY DIFFRACTIONr_bond_other_d0.0020.023254
X-RAY DIFFRACTIONr_angle_refined_deg1.9971.9864666
X-RAY DIFFRACTIONr_angle_other_deg1.70537504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6955456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.82821.626123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27715517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7981539
X-RAY DIFFRACTIONr_chiral_restr0.1360.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023840
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02682
X-RAY DIFFRACTIONr_nbd_refined0.240.2704
X-RAY DIFFRACTIONr_nbd_other0.1990.23342
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21661
X-RAY DIFFRACTIONr_nbtor_other0.0940.22099
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2470.2410
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0340.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.275
X-RAY DIFFRACTIONr_mcbond_it2.3321.52837
X-RAY DIFFRACTIONr_mcbond_other1.2331.5917
X-RAY DIFFRACTIONr_mcangle_it2.79723617
X-RAY DIFFRACTIONr_scbond_it3.72831260
X-RAY DIFFRACTIONr_scangle_it5.0344.51048
X-RAY DIFFRACTIONr_rigid_bond_restr2.36333708
X-RAY DIFFRACTIONr_sphericity_bonded4.98733025
LS refinement shellResolution: 1.15→1.176 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 385 -
Rwork0.245 7853 -
obs-7853 83.81 %

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