[English] 日本語
Yorodumi- PDB-4jpx: Crystal structure of phenylalanine hydroxylase S203P mutant from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jpx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of phenylalanine hydroxylase S203P mutant from Chromobacterium violaceum | ||||||
Components | Phenylalanine-4-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / hydroxylase | ||||||
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: 1.55 Å | ||||||
Authors | Ronau, J.A. / Abu-Omar, M.M. / Das, C. | ||||||
Citation | Journal: Eur.Biophys.J. / Year: 2013 Title: An additional substrate binding site in a bacterial phenylalanine hydroxylase. Authors: Ronau, J.A. / Paul, L.N. / Fuchs, J.E. / Corn, I.R. / Wagner, K.T. / Liedl, K.R. / Abu-Omar, M.M. / Das, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4jpx.cif.gz | 134.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4jpx.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jpx_validation.pdf.gz | 442.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4jpx_full_validation.pdf.gz | 443.7 KB | Display | |
Data in XML | 4jpx_validation.xml.gz | 14 KB | Display | |
Data in CIF | 4jpx_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/4jpx ftp://data.pdbj.org/pub/pdb/validation_reports/jp/4jpx | HTTPS FTP |
-Related structure data
Related structure data | 3tcyC 3tk2C 3tk4C 4esmC 4etlC 4jpyC 1ltuS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34049.457 Da / Num. of mol.: 1 / Mutation: S203P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium violaceum (bacteria) Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757 Gene: CV_3180, phhA / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P30967, phenylalanine 4-monooxygenase |
---|---|
#2: Chemical | ChemComp-PHE / |
#3: Chemical | ChemComp-CO / |
#4: Water | ChemComp-HOH / |
Sequence details | ACCORDING TO UNIPROT SEQUENCE DATABASE, THERE ARE SEQUENCE CONFLICTS AT THESE POSITIONS. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.16 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Na-HEPES, 0.001 M Magnesium chloride hexahydrate, 0.005 M Nickel (II) chloride hexahydrate, 15% w/v PEG 3,350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 23, 2011 |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 31409 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.6 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.55→1.58 Å / % possible all: 81.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1LTU Resolution: 1.55→22.74 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.436 / SU ML: 0.057 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 20.856 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→22.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|