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Yorodumi- PDB-2yap: X-ray induced reduction of laccase from Thermus thermophilus HB27... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yap | ||||||
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Title | X-ray induced reduction of laccase from Thermus thermophilus HB27 (62. 5-75.0 percent dose) | ||||||
Components | LACCASE | ||||||
Keywords | OXIDOREDUCTASE / MULTICOPPER OXIDASES | ||||||
Function / homology | Function and homology information hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Serrano-Posada, H. / Rudino-Pinera, E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: X-Ray-Induced Catalytic Active-Site Reduction of a Multicopper Oxidase: Structural Insights Into the Proton-Relay Mechanism and O2-Reduction States. Authors: Serrano-Posada, H. / Centeno-Leija, S. / Rojas-Trejo, S.P. / Rodriguez-Almazan, C. / Stojanoff, V. / Rudino-Pinera, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yap.cif.gz | 126.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yap.ent.gz | 97.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/2yap ftp://data.pdbj.org/pub/pdb/validation_reports/ya/2yap | HTTPS FTP |
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-Related structure data
Related structure data | 2xu9SC 2xuwC 2xvbC 2yaeC 2yafC 2yahC 2yamC 2yaoC 2yaqC 2yarC 4ai7C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 48791.457 Da / Num. of mol.: 1 / Fragment: MATURE FORM, RESIDUES 24-462 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q72HW2, laccase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-MRD / ( #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE AT THE UNIPROT DEPOSIT Q72HW2 POSITION 53 IS OCCUPIED BY A LEUCINE BUT THE ELECTRON ...THE SEQUENCE AT THE UNIPROT DEPOSIT Q72HW2 POSITION 53 IS OCCUPIED BY A LEUCINE BUT THE ELECTRON DENSITY CLEARLY SUPPORTS THE PRESENCE OF AN ISOLEUCINE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 8 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.62 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1M HEPES PH 7.5, 70% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2010 Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING. |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29 Å / Num. obs: 44430 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.1 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XU9 Resolution: 1.8→27.869 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 15.39 / Stereochemistry target values: ML Details: HIS 95 WAS REFINED AS THE SINGLE MEMBER OF A TLS GROUP.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.077 Å2 / ksol: 0.362 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→27.869 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -15.9241 Å / Origin y: -19.8604 Å / Origin z: 3.8287 Å
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Refinement TLS group | Selection details: RESID 95 AND CHAIN A |