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- PDB-2g85: Crystal structure of chorismate synthase from Mycobacterium tuber... -

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Basic information

Entry
Database: PDB / ID: 2g85
TitleCrystal structure of chorismate synthase from Mycobacterium tuberculosis at 2.22 angstrons of resolution
ComponentsChorismate synthase
KeywordsLYASE / beta-alpha-beta / shikimate pathway
Function / homology
Function and homology information


chorismate synthase / chorismate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / oxidoreductase activity, acting on NAD(P)H / 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: 2.22 Å
AuthorsDias, M.V.B. / dos Santos, B.B. / Ely, F. / Basso, L.A. / Santos, D.S. / de Azevedo Jr., W.F.
CitationJournal: To be Published
Title: Crystal structure of chorismate synthase from Mycobacterium tuberculosis at 2.22 angstron of resolution
Authors: Dias, M.V.B. / dos Santos, B.B. / Ely, F. / Basso, L.A. / Santos, D.S. / de Azevedo Jr., W.F.
History
DepositionMar 1, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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
Water7,584421
1
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_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area26300 Å2
ΔGint-113 kcal/mol
Surface area46150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.288, 130.288, 157.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-754-

HOH

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Components

#1: Protein Chorismate synthase / 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 / 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.: 421 / 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: 4.62 Å3/Da / Density % sol: 73.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1M Hepes-Na pH 7.8 buffer, 4M sodim chlorate , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2.22→50.25 Å / Num. all: 37755 / Num. obs: 37564 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 4.5 % / Num. unique all: 5036 / % possible all: 22

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZTB

1ztb


Resolution: 2.22→47.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.059 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.151 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21441 1873 5 %RANDOM
Rwork0.17318 ---
all0.17528 39553 --
obs0.1732 35623 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.825 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.22→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 0 421 3250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222875
X-RAY DIFFRACTIONr_angle_refined_deg2.2861.9653905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.735384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78122.437119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.29915445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.511533
X-RAY DIFFRACTIONr_chiral_restr0.2040.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022209
X-RAY DIFFRACTIONr_nbd_refined0.3050.21762
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21989
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.330.2411
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.2210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4550.278
X-RAY DIFFRACTIONr_mcbond_it1.4851.51937
X-RAY DIFFRACTIONr_mcangle_it2.38923030
X-RAY DIFFRACTIONr_scbond_it3.97231016
X-RAY DIFFRACTIONr_scangle_it6.0254.5875
LS refinement shellResolution: 2.222→2.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 122 -
Rwork0.281 2320 -
obs--85 %

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