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- PDB-1ztb: Crystal Structure of Chorismate Synthase from Mycobacterium tuber... -

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Basic information

Entry
Database: PDB / ID: 1ztb
TitleCrystal Structure of Chorismate Synthase from Mycobacterium tuberculosis
ComponentsChorismate synthase
KeywordsLIGASE / BETA-ALPHA-BETA / FLAVOPROTEIN / SHIKIMATE
Function / homology
Function and homology information


chorismate synthase / chorismate synthase activity / Chorismate via Shikimate Pathway / oxidoreductase activity, acting on NAD(P)H / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NAD binding / FMN binding / cytosol
Similarity search - Function
Chorismate synthase signature 3. / Chorismate synthase, AroC fold / Chorismate synthase AroC / Chorismate synthase signature 2. / Chorismate synthase / Chorismate synthase, conserved site / Chorismate synthase AroC superfamily / Chorismate synthase / Chorismate synthase signature 1. / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chorismate synthase / Chorismate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsDias, M.V.B. / Borges, J.C. / Ely, F. / Pereira, J.H. / Canduri, F. / Ramos, C.H.I. / Frazzon, J. / Palma, M.S. / Basso, L.A. / Santos, D.S. / Azevedo Jr., W.F.
CitationJournal: J.Struct.Biol. / Year: 2006
Title: Structure of chorismate synthase from Mycobacterium tuberculosis
Authors: Dias, M.V.B. / Borges, J.C. / Ely, F. / Pereira, J.H. / Canduri, F. / Ramos, C.H.I. / Frazzon, J. / Palma, M.S. / Basso, L.A. / Santos, D.S. / de Azevedo Jr., W.F.
History
DepositionMay 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chorismate synthase


Theoretical massNumber of molelcules
Total (without water)41,8441
Polymers41,8441
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Chorismate synthase

A: Chorismate synthase

A: Chorismate synthase

A: Chorismate synthase


Theoretical massNumber of molelcules
Total (without water)167,3784
Polymers167,3784
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area25930 Å2
ΔGint-110 kcal/mol
Surface area45300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)129.756, 129.756, 156.795
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Cell settinghexagonal
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-578-

HOH

21A-588-

HOH

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Components

#1: Protein Chorismate synthase / E.C.4.2.3.5 / 5-enolpyruvylshikimate-3-phosphate phospholyase


Mass: 41844.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: aroC, aroF / Plasmid: pET-23a(+) / Production host: Escherichia coli (E. coli)
References: UniProt: P63611, UniProt: P9WPY1*PLUS, chorismate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 4.55 Å3/Da / Density % sol: 72.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 400, magnesium chloride, Hepes, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 22, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2.65→52.93 Å / Num. all: 22658 / Num. obs: 22383 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.65→2.79 Å / Rmerge(I) obs: 0.337 / Num. unique all: 3129 / % possible all: 95.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.2refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QXO

1qxo


Resolution: 2.65→52.93 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.277 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.284 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22118 2290 10.2 %RANDOM
Rwork0.16193 ---
all0.204 22383 --
obs0.16803 20093 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.902 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.65→52.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2838 0 0 243 3081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222885
X-RAY DIFFRACTIONr_angle_refined_deg2.6551.9673919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2925386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49822.353119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.04415447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.871534
X-RAY DIFFRACTIONr_chiral_restr0.190.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022223
X-RAY DIFFRACTIONr_nbd_refined0.3170.31841
X-RAY DIFFRACTIONr_nbtor_refined0.360.52018
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.5424
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.3210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3030.566
X-RAY DIFFRACTIONr_mcbond_it3.77321946
X-RAY DIFFRACTIONr_mcangle_it5.4533046
X-RAY DIFFRACTIONr_scbond_it4.84221016
X-RAY DIFFRACTIONr_scangle_it7.0853873
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 172 -
Rwork0.3 1409 -
obs--93.49 %

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