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- PDB-1umf: crystal structure of chorismate synthase -

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Basic information

Entry
Database: PDB / ID: 1umf
Titlecrystal structure of chorismate synthase
ComponentsChorismate synthase
KeywordsLYASE / BETA-ALPHA-BETA SANDWICH FOLD
Function / homology
Function and homology information


chorismate synthase / chorismate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / 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
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAhn, H.J. / Yoon, H.J. / Lee, B. / Suh, S.W.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of chorismate synthase: a novel FMN-binding protein fold and functional insights
Authors: Ahn, H.J. / Yoon, H.J. / Lee, B. / Suh, S.W.
History
DepositionSep 30, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chorismate synthase
B: Chorismate synthase
C: Chorismate synthase
D: Chorismate synthase


Theoretical massNumber of molelcules
Total (without water)160,6204
Polymers160,6204
Non-polymers00
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26800 Å2
ΔGint-162 kcal/mol
Surface area52780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.478, 146.478, 132.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
Chorismate synthase / 5-enolpyruvylshikimate-3-phosphate phospholyase


Mass: 40154.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P56122, chorismate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.15 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 400, CaCl2, HEPES, DTT, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Apr 10, 2003 / Details: mirrors
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 64913 / Num. obs: 64913 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.9 Å2
Reflection shellResolution: 2.25→2.39 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→21.13 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4124287.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 6567 10.1 %RANDOM
Rwork0.202 ---
obs0.202 64913 98.5 %-
all-64913 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.9538 Å2 / ksol: 0.378737 e/Å3
Displacement parametersBiso mean: 50.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.69 Å20 Å20 Å2
2---5.69 Å20 Å2
3---11.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.25→21.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11264 0 0 492 11756
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 1090 10.2 %
Rwork0.257 9631 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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