+Open data
-Basic information
Entry | Database: PDB / ID: 1g81 | ||||||
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Title | CHORISMATE LYASE WITH BOUND PRODUCT, ORTHORHOMBIC CRYSTAL FORM | ||||||
Components | CHORISMATE LYASE | ||||||
Keywords | LYASE / NEW FOLD / UBIQUINONE PATHWAY / 123654 ANTIPARALLEL SHEET TOPOLOGY / PRODUCT INHIBITION | ||||||
Function / homology | Function and homology information chorismate lyase / chorismate lyase activity / pyruvate biosynthetic process / ubiquinone biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.71 Å | ||||||
Authors | Gallagher, D.T. / Mayhew, M. / Holden, M.J. / Vilker, V.L. / Howard, A. | ||||||
Citation | Journal: Proteins / Year: 2001 Title: The crystal structure of chorismate lyase shows a new fold and a tightly retained product. Authors: Gallagher, D.T. / Mayhew, M. / Holden, M.J. / Howard, A. / Kim, K.J. / Vilker, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g81.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g81.ent.gz | 34 KB | Display | PDB format |
PDBx/mmJSON format | 1g81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g81_validation.pdf.gz | 439.6 KB | Display | wwPDB validaton report |
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Full document | 1g81_full_validation.pdf.gz | 441.6 KB | Display | |
Data in XML | 1g81_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1g81_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/1g81 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/1g81 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | ENZYME IS A MONOMER |
-Components
#1: Protein | Mass: 18651.621 Da / Num. of mol.: 1 / Mutation: C14S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: UBIC / Production host: Escherichia coli (E. coli) / References: UniProt: P26602, Lyases |
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#2: Chemical | ChemComp-PHB / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.55 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 26% PEG 4K, 80 mM Hepes, 5% Isopropanol, 5mM PHB, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion / Details: Stover, C., (2000) J. Struct. Biol., 129, 96. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9879 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9879 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 15812 / Num. obs: 15812 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.12 / % possible all: 83 |
Reflection | *PLUS % possible obs: 95 % / Num. measured all: 63214 |
Reflection shell | *PLUS % possible obs: 83 % |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.71→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 481823.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 74.79 Å2 / ksol: 0.444 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.71→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.78 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.2 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.261 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.242 / Rfactor obs: 0.25 |