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Yorodumi- PDB-3kbr: The crystal structure of cyclohexadienyl dehydratase precursor fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kbr | ||||||
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Title | The crystal structure of cyclohexadienyl dehydratase precursor from Pseudomonas aeruginosa PA01 | ||||||
Components | Cyclohexadienyl dehydratase | ||||||
Keywords | LYASE / cyclohexadienyl dehydratase precursor / Pseudomonas aeruginosa PA01 / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / Multifunctional enzyme / Phenylalanine biosynthesis | ||||||
Function / homology | Function and homology information arogenate dehydratase / arogenate dehydratase activity / prephenate dehydratase / prephenate dehydratase activity / L-phenylalanine biosynthetic process / periplasmic space Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.659 Å | ||||||
Authors | Tan, K. / Marshall, N. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of cyclohexadienyl dehydratase precursor from Pseudomonas aeruginosa PA01 Authors: Tan, K. / Marshall, N. / Buck, K. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kbr.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kbr.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kbr_validation.pdf.gz | 460.9 KB | Display | wwPDB validaton report |
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Full document | 3kbr_full_validation.pdf.gz | 463.3 KB | Display | |
Data in XML | 3kbr_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3kbr_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/3kbr ftp://data.pdbj.org/pub/pdb/validation_reports/kb/3kbr | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Experimentally unknown. It is predicted to be monomeric. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27635.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: PA3475, pheC, Pseudomonas aeruginosa / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 References: UniProt: Q01269, prephenate dehydratase, arogenate dehydratase |
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-Non-polymers , 6 types, 173 molecules
#2: Chemical | ChemComp-NI / | ||||||
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#3: Chemical | ChemComp-CL / | ||||||
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-EPE / | #7: 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: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.005M CoCl2 hexahydrate, 0.005M NiCl2 hexahydrate, 0.005M CaCl2 dihydrate, 0.005M MgCl2 hexahydrate, 0.1M HEPES, 12% w/v PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2009 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 |
Reflection | Resolution: 1.659→28.8 Å / Num. all: 32048 / Num. obs: 32048 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 37.1 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1.75 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.659→28.732 Å / SU ML: 0.21 / σ(F): 1.9 / Phase error: 24.55 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.051 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.659→28.732 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: chain A resid 124:215 |