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- PDB-4csm: YEAST CHORISMATE MUTASE + TYR + ENDOOXABICYCLIC INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 4csm
TitleYEAST CHORISMATE MUTASE + TYR + ENDOOXABICYCLIC INHIBITOR
ComponentsCHORISMATE MUTASE
KeywordsCOMPLEX (ISOMERASE/PEPTIDE) / CHORISMATE PYRUVATE MUTASE / ALLOSTERIC PROTEIN / COMPLEX (ISOMERASE-PEPTIDE) / TRANSITION STATE ANALOG / COMPLEX (ISOMERASE-PEPTIDE) complex
Function / homology
Function and homology information


tryptophan binding / L-tyrosine binding / L-tyrosine biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / L-phenylalanine biosynthetic process / aromatic amino acid family biosynthetic process / nucleus / cytoplasm
Similarity search - Function
Chorismate Mutase, subunit A / Chorismate mutase, AroQ class superfamily, eukaryotic / Chorismate mutase, AroQ class, eukaryotic type / Chorismate mutase domain profile. / Chorismate mutase, AroQ class superfamily, eukaryotic / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-TSA / TYROSINE / Chorismate mutase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStraeter, N. / Schnappauf, G. / Braus, G. / Lipscomb, W.N.
Citation
Journal: Structure / Year: 1997
Title: Mechanisms of catalysis and allosteric regulation of yeast chorismate mutase from crystal structures.
Authors: Strater, N. / Schnappauf, G. / Braus, G. / Lipscomb, W.N.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Crystal Structure of the T State of Allosteric Yeast Chorismate Mutase and Comparison with the R State
Authors: Strater, N. / Hakansson, K. / Schnappauf, G. / Braus, G. / Lipscomb, W.N.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Location of the Active Site of Allosteric Chorismate Mutase from Saccharomyces Cerevisiae, and Comments on the Catalytic and Regulatory Mechanisms
Authors: Xue, Y. / Lipscomb, W.N.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: The Crystal Structure of Allosteric Chorismate Mutase at 2.2-A Resolution
Authors: Xue, Y. / Lipscomb, W.N. / Graf, R. / Schnappauf, G. / Braus, G.
History
DepositionJul 14, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / 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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHORISMATE MUTASE
B: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3976
Polymers59,5782
Non-polymers8194
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHORISMATE MUTASE
hetero molecules

B: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3976
Polymers59,5782
Non-polymers8194
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4870 Å2
ΔGint-19 kcal/mol
Surface area22210 Å2
MethodPISA
3
A: CHORISMATE MUTASE
hetero molecules

A: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3976
Polymers59,5782
Non-polymers8194
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area4800 Å2
ΔGint-20 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.500, 205.500, 131.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO SUBUNITS OF THE PROTEIN. THE SUBUNITS WERE REFINED USING RESTRAINTS. THE TWO SUBUNITS BELONG TO DIFFERENT DIMERS.

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Components

#1: Protein CHORISMATE MUTASE / CHORISMATE PYRUVATE MUTASE


Mass: 29789.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: RH1242 / Plasmid: PME605 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): RH1242 / References: UniProt: P32178, chorismate mutase
#2: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3 / Details: TYROSINE BOUND TO REGULATORY SITE
#3: Chemical ChemComp-TSA / 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID


Mass: 228.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12O6

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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: 4.5 Å3/Da / Density % sol: 72.49 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9
Details: HANGING DROP, 32 % (W/V) PEG MONOMETHYLETHER 500, 4 MM DTT, 0.1 M TRIS PH 9.0, 0.1 M SODIUM CHLORIDE, 2 MM TYROSINE, 3 MM INHIBITOR, 10 MG/ML PROTEIN, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
23 mMendo-oxabicyclic inhibitor1drop
332 %(w/v)mPEG5501reservoir
44 mMdithiothreitol1reservoir
50.1 MTris-HCl1reservoir
60.1 Msodium chloride1reservoir
72 mMtyrosine1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 12, 1997 / Details: SUPPER DOUBLE-MIRROR, NI-COATED
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 25765 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.084
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.291 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 64883
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CSM

1csm


Resolution: 2.8→15 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.27 -8 %RANDOM
Rwork0.213 ---
obs0.213 22397 --
Displacement parametersBiso mean: 40.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4144 0 58 0 4202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d18.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.36 -8 %
Rwork0.287 2090 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6
LS refinement shell
*PLUS
Lowest resolution: 2.9 Å / Rfactor obs: 0.287

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