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Yorodumi- PDB-4q3w: Crystal structure of C. violaceum phenylalanine hydroxylase D139E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q3w | ||||||
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Title | Crystal structure of C. violaceum phenylalanine hydroxylase D139E mutation | ||||||
Components | Phenylalanine-4-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / Mutation / hydroxylase / phenylalanine hydroxylase / kinetics / metals / Chromobacterium / phenylketonurias / biopterin / Mixed alpha helix-beta sheet | ||||||
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: 1.4 Å | ||||||
Authors | Ronau, J.A. / Abu-Omar, M.M. / Das, C. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: A conserved acidic residue in phenylalanine hydroxylase contributes to cofactor affinity and catalysis. Authors: Ronau, J.A. / Paul, L.N. / Fuchs, J.E. / Liedl, K.R. / Abu-Omar, M.M. / Das, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q3w.cif.gz | 131.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q3w.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 4q3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q3w_validation.pdf.gz | 433.2 KB | Display | wwPDB validaton report |
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Full document | 4q3w_full_validation.pdf.gz | 434.2 KB | Display | |
Data in XML | 4q3w_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 4q3w_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/4q3w ftp://data.pdbj.org/pub/pdb/validation_reports/q3/4q3w | HTTPS FTP |
-Related structure data
Related structure data | 4q3xC 4q3yC 4q3zC 1ltuS C: citing same article (ref.) S: Starting model for refinement |
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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: 33661.043 Da / Num. of mol.: 1 / Mutation: D139E 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: phhA, CV_3180 / Plasmid: pET3a / 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-CO / |
#3: Chemical | ChemComp-EDO / |
#4: 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: 1.89 Å3/Da / Density % sol: 34.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM Na-HEPES, pH 7.0, 10 mM Magnesium chloride hexahydrate, 5 mM Nickel(II) chloride hexahydrate, 15% w/v polyethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: Mar 16, 2013 |
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: 1.4→50 Å / Num. all: 46304 / Num. obs: 44359 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.4→1.42 Å / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1LTU Resolution: 1.4→22.81 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.319 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.067 / 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: 16.149 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→22.81 Å
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Refine LS restraints |
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