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Yorodumi- PDB-5zrd: Tyrosinase from Burkholderia thailandensis (BtTYR) at low pH condition -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zrd | ||||||
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Title | Tyrosinase from Burkholderia thailandensis (BtTYR) at low pH condition | ||||||
Components | Tyrosinase | ||||||
Keywords | OXIDOREDUCTASE / Tyrosinase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia thailandensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Lee, S. / Son, H.-F. / Kim, K.-J. | ||||||
Citation | Journal: Acs Catalysis / Year: 2018 Title: Structural Basis for Highly Efficient Production of Catechol Derivatives at Acidic pH by Tyrosinase from Burkholderia thailandensis Authors: Son, H.F. / Lee, S.H. / Lee, S.H. / Kim, H. / Hong, H. / Lee, U.J. / Lee, P.G. / Kim, B.G. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zrd.cif.gz | 426.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zrd.ent.gz | 349.4 KB | Display | PDB format |
PDBx/mmJSON format | 5zrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zrd_validation.pdf.gz | 508.5 KB | Display | wwPDB validaton report |
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Full document | 5zrd_full_validation.pdf.gz | 550.7 KB | Display | |
Data in XML | 5zrd_validation.xml.gz | 82 KB | Display | |
Data in CIF | 5zrd_validation.cif.gz | 112.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/5zrd ftp://data.pdbj.org/pub/pdb/validation_reports/zr/5zrd | HTTPS FTP |
-Related structure data
Related structure data | 5zreSC 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 60674.969 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264) (bacteria) Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: melO, BTH_II0649, DR63_5120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2T7K1, tyrosinase |
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-Non-polymers , 5 types, 547 molecules
#2: Chemical | ChemComp-CIT / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CU / #5: Chemical | ChemComp-O / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 22% (v/v) reagent alcohol, 100 mM sodium citrate dibasic, pH 4.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→123.8 Å / Num. obs: 131667 / % possible obs: 97.8 % / Redundancy: 8.1 % / Rsym value: 0.07 / Net I/σ(I): 39.95 |
Reflection shell | Resolution: 2.3→2.34 Å / Rsym value: 0.306 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZRE Resolution: 2.3→28.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.153 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.194 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 185.5 Å2 / Biso mean: 47.944 Å2 / Biso min: 21.94 Å2
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Refinement step | Cycle: final / Resolution: 2.3→28.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.302→2.362 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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