[English] 日本語
Yorodumi- PDB-1ltv: CRYSTAL STRUCTURE OF CHROMOBACTERIUM VIOLACEUM PHENYLALANINE HYDR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ltv | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF CHROMOBACTERIUM VIOLACEUM PHENYLALANINE HYDROXYLASE, STRUCTURE WITH BOUND OXIDIZED Fe(III) | ||||||
Components | PHENYLALANINE-4-HYDROXYLASE | ||||||
Keywords | OXIDOREDUCTASE / phenylalanine hydroxylase / iron-bound / catalytic core | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ltv.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ltv.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ltv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/1ltv ftp://data.pdbj.org/pub/pdb/validation_reports/lt/1ltv | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ltuSC 1ltzC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.09 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium sufate, NaCl, HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2000 |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 19978 / Num. obs: 17224 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.081 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1107 / Rsym value: 0.334 / % possible all: 56.5 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. obs: 17967 / Num. measured all: 51451 |
Reflection shell | *PLUS % possible obs: 56.5 % / Redundancy: 0 % |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LTU Resolution: 2→20 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 2.9 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.07 Å
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|