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Yorodumi- PDB-2qmx: The crystal structure of L-Phe inhibited prephenate dehydratase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qmx | ||||||
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Title | The crystal structure of L-Phe inhibited prephenate dehydratase from Chlorobium tepidum TLS | ||||||
Components | Prephenate dehydratase | ||||||
Keywords | LIGASE / APC86053 / L-Phe inhibition / prephenate dehydratase / PDT / Chlorobium tepidum TLS / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Lyase | ||||||
Function / homology | Function and homology information prephenate dehydratase / prephenate dehydratase activity / chorismate mutase activity / L-phenylalanine biosynthetic process Similarity search - Function | ||||||
Biological species | Chlorobium tepidum TLS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Tan, K. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2008 Title: Structures of open (R) and close (T) states of prephenate dehydratase (PDT) - implication of allosteric regulation by L-phenylalanine. Authors: Tan, K. / Li, H. / Zhang, R. / Gu, M. / Clancy, S.T. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qmx.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qmx.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 2qmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qmx_validation.pdf.gz | 482.4 KB | Display | wwPDB validaton report |
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Full document | 2qmx_full_validation.pdf.gz | 509.3 KB | Display | |
Data in XML | 2qmx_validation.xml.gz | 25 KB | Display | |
Data in CIF | 2qmx_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/2qmx ftp://data.pdbj.org/pub/pdb/validation_reports/qm/2qmx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Chains A and B form a dimer. The dimer and its symmetry-related dimer (-x,-y,z) form a tetramer. |
-Components
#1: Protein | Mass: 31596.154 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorobium tepidum TLS (bacteria) / Species: Chlorobaculum tepidum / Strain: TLS, DSM 12025 / Gene: pheA, CT1666 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8KBW6, prephenate dehydratase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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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: 2.49 Å3/Da / Density % sol: 50.55 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 30% v/v PEG 400, 0.1M Acetate, 0.2M Calcium Acetate, pH 4.5, 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: 0.97918, 0.97932 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2007 / Details: Mirror | |||||||||
Radiation | Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→41.13 Å / Num. all: 23798 / Num. obs: 23798 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 35.5 | |||||||||
Reflection shell | Resolution: 2.3→2.37 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1245 / % possible all: 52.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→41.13 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.895 / SU B: 17.822 / SU ML: 0.21 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.547 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.497 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→41.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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