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Yorodumi- PDB-2xvb: Crystal structure of Laccase from Thermus thermophilus HB27 compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xvb | ||||||
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Title | Crystal structure of Laccase from Thermus thermophilus HB27 complexed with Hg, crystal of the apoenzyme soaked for 5 min. in 5 mM HgCl2 at 278 K. | ||||||
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: 1.7 Å | ||||||
Authors | Serrano-Posada, H. / Valderrama, B. / 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 | 2xvb.cif.gz | 125.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xvb.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/2xvb ftp://data.pdbj.org/pub/pdb/validation_reports/xv/2xvb | HTTPS FTP |
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-Related structure data
Related structure data | 2xu9SC 2xuwC 2yaeC 2yafC 2yahC 2yamC 2yaoC 2yapC 2yaqC 2yarC 4ai7C 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 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 / Plasmid: PET32A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q72HW2, laccase | ||||||||
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#2: Chemical | ChemComp-HG / #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-MRD / ( #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE AT THE UNIPROT POSITION 53 IS OCCUPIED BY A LEUCINE BUT THE ELECTRON DENSITY CLEARLY ...THE SEQUENCE AT THE UNIPROT 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.36 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M HEPES PH 7.5,70 % MPD. BEFORE DATA COLLECTION THE CRYSTAL WAS SOAKED FOR 5 MINUTES IN 5 MM HGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8321 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 23, 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: 0.8321 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 59564 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 15.75 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.14 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.72 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XU9 Resolution: 1.7→19.689 Å / SU ML: 0.17 / σ(F): 1.91 / Phase error: 15.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.572 Å2 / ksol: 0.369 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.986 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.689 Å
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Refine LS restraints |
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LS refinement shell |
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