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- PDB-1csm: THE CRYSTAL STRUCTURE OF ALLOSTERIC CHORISMATE MUTASE AT 2.2 ANGS... -

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Basic information

Entry
Database: PDB / ID: 1csm
TitleTHE CRYSTAL STRUCTURE OF ALLOSTERIC CHORISMATE MUTASE AT 2.2 ANGSTROMS RESOLUTION
ComponentsCHORISMATE MUTASE
KeywordsISOMERASE
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 / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TRYPTOPHAN / Chorismate mutase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsXue, Y. / Lipscomb, W.N.
CitationJournal: 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
DepositionAug 22, 1994Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_ref_seq_dif / 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_ref_seq_dif.details / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,0114
Polymers59,6022
Non-polymers4082
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-22 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.800, 95.800, 157.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein CHORISMATE MUTASE


Mass: 29801.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P32178
#2: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Mutation: ALLELE MUTANT, THR 226 ILE / Source method: obtained synthetically / Formula: C11H12N2O2 / References: anthranilate synthase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Xue, Y., (1994) J. Mol. Biol., 241, 273. / PH range low: 8.5 / PH range high: 5.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
255 %(w/v)satammonium sulfate1reservoir
350 mMTris-HCl1reservoir
42 mMDTT1reservoir
50.1 mMEDTA1reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 19, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 38840 / % possible obs: 80.6 % / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Rmerge(I) obs: 0.086
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 83251 / Rmerge(I) obs: 0.086

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Processing

Software
NameClassification
MSCdata collection
X-PLORmodel building
X-PLORrefinement
MSCdata reduction
X-PLORphasing
RefinementResolution: 2.2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.31 --
Rwork0.196 --
obs0.196 38840 80.1 %
Displacement parametersBiso mean: 32.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5110 0 0 291 5401
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.11
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_deg1.527
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.73
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.463
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

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