+Open data
-Basic information
Entry | Database: PDB / ID: 4csm | ||||||
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Title | YEAST CHORISMATE MUTASE + TYR + ENDOOXABICYCLIC INHIBITOR | ||||||
Components | CHORISMATE MUTASE | ||||||
Keywords | COMPLEX (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 / 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 | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Straeter, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4csm.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4csm.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 4csm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4csm_validation.pdf.gz | 412 KB | Display | wwPDB validaton report |
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Full document | 4csm_full_validation.pdf.gz | 424.8 KB | Display | |
Data in XML | 4csm_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 4csm_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/4csm ftp://data.pdbj.org/pub/pdb/validation_reports/cs/4csm | HTTPS FTP |
-Related structure data
Related structure data | 3csmC 5csmC 1csmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | THE ASYMMETRIC UNIT CONTAINS TWO SUBUNITS OF THE PROTEIN. THE SUBUNITS WERE REFINED USING RESTRAINTS. THE TWO SUBUNITS BELONG TO DIFFERENT DIMERS. |
-Components
#1: Protein | 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 | #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72.49 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: 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
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Mar 12, 1997 / Details: SUPPER DOUBLE-MIRROR, NI-COATED |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CSM Resolution: 2.8→15 Å / σ(F): 2
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Displacement parameters | Biso mean: 40.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.93 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.9 Å / Rfactor obs: 0.287 |