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- PDB-2csm: TYR-BOUND T-STATE OF YEAST CHORISMATE MUTASE -

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Basic information

Entry
Database: PDB / ID: 2csm
TitleTYR-BOUND T-STATE OF YEAST CHORISMATE MUTASE
ComponentsCHORISMATE MUTASE
KeywordsCOMPLEX (ISOMERASE/PEPTIDE) / ALLOSTERIC PROTEIN / COMPLEX (ISOMERASE-PEPTIDE) / 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
TYROSINE / Chorismate mutase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsStraeter, N. / Hakansson, K. / Lipscomb, W.N.
Citation
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.
#1: 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.
#2: 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
DepositionNov 24, 1995Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,9702
Polymers29,7891
Non-polymers1811
Water55831
1
A: CHORISMATE MUTASE
hetero molecules

A: CHORISMATE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9414
Polymers59,5782
Non-polymers3622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Unit cell
Length a, b, c (Å)78.600, 78.600, 116.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CHORISMATE MUTASE / CHORISMATE PYRUVATE MUTASE


Mass: 29789.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32178, chorismate mutase
#2: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.1 Mammonium salfate1reservoir
255 mMsodium acetate1reservoir
32 mMdithiothreitol1reservoir
40.7 mML-tyrosine1reservoir
52.1 Mammonium salfate1drop
655 mMsodium acetate1drop
72 mMdithiothreitol1drop
80.7 mML-tyrosine1drop
915 mg/mlYCM1drop

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Date: Oct 10, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 9401 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.069
Reflection
*PLUS
Num. measured all: 29418
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.8→7 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.321 -10 %
Rwork0.213 --
obs0.213 8964 92.1 %
Displacement parametersBiso mean: 22.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 13 31 2056
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å

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