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- PDB-5csm: YEAST CHORISMATE MUTASE, T226S MUTANT, COMPLEX WITH TRP -

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Basic information

Entry
Database: PDB / ID: 5csm
TitleYEAST CHORISMATE MUTASE, T226S MUTANT, COMPLEX WITH TRP
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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TRYPTOPHAN / Chorismate mutase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1492
Polymers29,9441
Non-polymers2041
Water1,53185
1
A: CHORISMATE MUTASE
hetero molecules

A: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2974
Polymers59,8892
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4000 Å2
ΔGint-22 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.600, 51.400, 66.800
Angle α, β, γ (deg.)90.00, 116.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CHORISMATE MUTASE / / CHORISMATE PYRUVATE MUTASE


Mass: 29944.457 Da / Num. of mol.: 1 / Mutation: T226S
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 / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2 / Details: TRYPTOPHAN BOUND TO A REGULATORY SITE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.4 Å3/Da / Density % sol: 49.25 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: HANGING DROP, 19 % PEG 3350, 3 MM DTT, 0.16 M SODIUM ACETATE PH 5.0, 16 MM TRYPTOPHAN, 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
219 %PEG33501reservoir
33 mMdithiothreitol1reservoir
40.16 Msodium acetate1reservoir
516 mMtryptophan1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jun 27, 1996 / 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→30 Å / Num. obs: 18951 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.196 / % possible all: 88.8
Reflection
*PLUS
Num. measured all: 40918
Reflection shell
*PLUS
% possible obs: 88.8 %

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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: 2→7 Å / σ(F): 2
Details: RESIDUES THR 218 - GLU 223 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAPS (LOOP REGION). RESIDUES THR 218 - GLU 223 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAPS (LOOP REGION).
RfactorNum. reflection% reflectionSelection details
Rfree0.236 -8 %RANDOM
Rwork0.186 ---
obs0.186 17011 --
Displacement parametersBiso mean: 26.7 Å2
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 15 85 2151
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_d19.7
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
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.309 -8 %
Rwork0.255 1453 -
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_deg19.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6
LS refinement shell
*PLUS
Lowest resolution: 2.1 Å / Rfactor obs: 0.255

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