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- PDB-3csm: STRUCTURE OF YEAST CHORISMATE MUTASE WITH BOUND TRP AND AN ENDOOX... -

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Basic information

Entry
Database: PDB / ID: 3csm
TitleSTRUCTURE OF YEAST CHORISMATE MUTASE WITH BOUND TRP AND AN ENDOOXABICYCLIC INHIBITOR
ComponentsCHORISMATE MUTASE
KeywordsCOMPLEX (ISOMERASE/PEPTIDE) / CHORISMATE PYRUVATEMUTASE / 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
TRYPTOPHAN / Chem-TSA / Chorismate mutase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 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 10, 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 ...database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)60,7826
Polymers59,9172
Non-polymers8654
Water00
1


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

A: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7826
Polymers59,9172
Non-polymers8654
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area4650 Å2
ΔGint-18 kcal/mol
Surface area21700 Å2
MethodPISA
3
B: CHORISMATE MUTASE
hetero molecules

B: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7826
Polymers59,9172
Non-polymers8654
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4700 Å2
ΔGint-18 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.500, 203.500, 128.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein CHORISMATE MUTASE / CHORISMATE PYRUVATE MUTASE


Mass: 29958.484 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-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / Details: TRYPTOPHAN BOUND TO A 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: 4.3 Å3/Da / Density % sol: 71.24 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP, 19 % (W/V) PEG MONOMETHYLETHER 5000, 5 MM DTT, 0.15 M TRIS PH 8.0, 0.15 M SODIUM ACETATE, 16 MM TRYPTOPHAN, 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
319 %(w/v)mPEG50001reservoir
45 mMdithiothreitol1reservoir
50.15 MTris-HCl1reservoir
60.15 Msodium acetate1reservoir
716 mMtryptophan1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Oct 15, 1996 / Details: SUPPER DOUBLE-MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 20253 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.092
Reflection shellResolution: 3→3.2 Å / Rmerge(I) obs: 0.325 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 51388
Reflection shell
*PLUS
% possible obs: 99.1 %

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Processing

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

1csm


Resolution: 3→15 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.247 -8 %RANDOM
Rwork0.204 ---
obs0.204 16930 --
Displacement parametersBiso mean: 38.6 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4144 0 62 0 4206
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.0871.5
X-RAY DIFFRACTIONx_mcangle_it4.8562
X-RAY DIFFRACTIONx_scbond_it5.1442
X-RAY DIFFRACTIONx_scangle_it7.5232.5
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.363 -8 %
Rwork0.285 1470 -
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_deg19
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7
LS refinement shell
*PLUS
Lowest resolution: 3.2 Å / Rfactor obs: 0.285

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