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Yorodumi- PDB-1dii: CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE AT 2.5 A RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dii | |||||||||
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Title | CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE AT 2.5 A RESOLUTION | |||||||||
Components | (P-CRESOL METHYLHYDROXYLASE4-Cresol dehydrogenase (hydroxylating)) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / FLAVOCYTOCHROME / ELECTRON-TRANSFER / FAD / HEME | |||||||||
Function / homology | Function and homology information 4-methylphenol dehydrogenase (hydroxylating) / 4-cresol dehydrogenase (hydroxylating) activity / FAD binding / electron transfer activity / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Pseudomonas putida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | |||||||||
Authors | Cunane, L.M. / Chen, Z.W. / Shamala, N. / Mathews, F.S. / Cronin, C.N. / McIntire, W.S. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Structures of the flavocytochrome p-cresol methylhydroxylase and its enzyme-substrate complex: gated substrate entry and proton relays support the proposed catalytic mechanism. Authors: Cunane, L.M. / Chen, Z.W. / Shamala, N. / Mathews, F.S. / Cronin, C.N. / McIntire, W.S. #1: Journal: Biochemistry / Year: 1991 Title: Three-dimensional Structure of p-Cresol Methylhydroxylase (Flavocytochrome c) from Pseudomonas putida at 3.0 A Resolution Authors: Mathews, F.S. / Chen, Z.W. / Bellamy, H. / McIntire, W.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dii.cif.gz | 248.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dii.ent.gz | 207.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/1dii ftp://data.pdbj.org/pub/pdb/validation_reports/di/1dii | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | ASYMMETRIC UNIT CONTAINS A FLAVOPROTEIN DIMER RELATED BY A MOLECULAR 2-FOLD AXIS. TWO CYTOCHROME SUBUNITS ARE BOUND ON THE PERIPHERY OF THE FLAVOPROTEIN DIMER. |
-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 58005.965 Da / Num. of mol.: 2 / Fragment: FLAVOPROTEIN SUBUNIT / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / Cellular location: PERIPLASM / Strain: NCIMB 9869 / References: UniProt: P09788, EC: 1.17.99.1 #2: Protein | Mass: 8611.642 Da / Num. of mol.: 2 / Fragment: CYTOCHROME SUBUNIT / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / Cellular location: PERIPLASM / Strain: NCIMB 9869 / References: UniProt: P09787, EC: 1.17.99.1 |
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-Non-polymers , 4 types, 391 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.69 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 7 Details: PEG 8000, NA/K PHOSPHATE, NACL, pH 7.0, LIQUID DIFFUSION, temperature 298K | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 58 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: or interface diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: May 31, 1990 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 47875 / Num. obs: 42484 / % possible obs: 89.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.5→2.7 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.224 / % possible all: 87 |
Reflection shell | *PLUS % possible obs: 87 % |
-Processing
Software |
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Refinement | Resolution: 2.5→30 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.86 Å / Rfactor Rfree: 0.331 / Rfactor Rwork: 0.287 |