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Yorodumi- PDB-1ltz: CRYSTAL STRUCTURE OF CHROMOBACTERIUM VIOLACEUM PHENYLALANINE HYDR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ltz | ||||||
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Title | CRYSTAL STRUCTURE OF CHROMOBACTERIUM VIOLACEUM PHENYLALANINE HYDROXYLASE, STRUCTURE HAS BOUND IRON (III) AND OXIDIZED COFACTOR 7,8-DIHYDROBIOPTERIN | ||||||
Components | PHENYLALANINE-4-HYDROXYLASE | ||||||
Keywords | OXIDOREDUCTASE / HYDROXYLASE / PHENYLALANINE / DIHYDROBIOPTERIN / BACTERIAL ENZYME | ||||||
Function / homology | Function and homology information phenylalanine 4-monooxygenase / phenylalanine 4-monooxygenase activity / L-phenylalanine catabolic process / iron ion binding Similarity search - Function | ||||||
Biological species | Chromobacterium violaceum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Difference map / Resolution: 1.4 Å | ||||||
Authors | Erlandsen, H. / Kim, J.Y. / Patch, M.G. / Han, A. / Volner, A. / Abu-Omar, M.M. / Stevens, R.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Structural comparison of bacterial and human iron-dependent phenylalanine hydroxylases: similar fold, different stability and reaction rates. Authors: Erlandsen, H. / Kim, J.Y. / Patch, M.G. / Han, A. / Volner, A. / Abu-Omar, M.M. / Stevens, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ltz.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ltz.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ltz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/1ltz ftp://data.pdbj.org/pub/pdb/validation_reports/lt/1ltz | HTTPS FTP |
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-Related structure data
Related structure data | 1ltuSC 1ltvC 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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Unit cell |
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-Components
#1: Protein | Mass: 33627.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS / References: UniProt: P30967, phenylalanine 4-monooxygenase |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-HBI / |
#5: 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: 2.15 Å3/Da / Density % sol: 42.89 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, NaCl, HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. all: 54370 / Num. obs: 54730 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1910 / % possible all: 67.2 |
Reflection | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 20 Å / Redundancy: 9-12 / Num. measured all: 54730 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 67.2 % / Rmerge(I) obs: 0.427 |
-Processing
Software |
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Refinement | Method to determine structure: Difference map Starting model: PDB ENTRY 1LTU Resolution: 1.4→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS, SHELZ' / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.159 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 1.42 Å |