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Yorodumi- PDB-6q29: Crystal structure of Laccase from Thermus thermophilus HB27 with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q29 | ||||||
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Title | Crystal structure of Laccase from Thermus thermophilus HB27 with an open conformation of beta-hairpin (Average deposted dose 2.5 MGy) | ||||||
Components | Laccase | ||||||
Keywords | STRUCTURAL PROTEIN / open loop / multicopper oxidase | ||||||
Function / homology | Function and homology information hydroquinone:oxygen oxidoreductase activity / laccase / ferroxidase activity / outer membrane-bounded periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.702 Å | ||||||
Authors | Miranda-Blancas, R. / Rudino-Pinera, E. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2021 Title: The beta-hairpin from the Thermus thermophilus HB27 laccase works as a pH-dependent switch to regulate laccase activity. Authors: Miranda-Blancas, R. / Avelar, M. / Rodriguez-Arteaga, A. / Sinicropi, A. / 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 | 6q29.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q29.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 6q29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q29_validation.pdf.gz | 438.9 KB | Display | wwPDB validaton report |
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Full document | 6q29_full_validation.pdf.gz | 441.7 KB | Display | |
Data in XML | 6q29_validation.xml.gz | 22 KB | Display | |
Data in CIF | 6q29_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/6q29 ftp://data.pdbj.org/pub/pdb/validation_reports/q2/6q29 | HTTPS FTP |
-Related structure data
Related structure data | 6tyrC 5xu9S 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
#1: Protein | Mass: 48791.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1370 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q72HW2, laccase | ||||
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#2: Chemical | ChemComp-PG4 / | ||||
#3: Chemical | ChemComp-PGE / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.12 % / Description: triangular shaped sheets |
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Crystal grow | Temperature: 277.15 K / Method: batch mode / pH: 5.5 Details: 20% PEG 4000, 20% 2-propanol, 100 mM Citrate buffer PH range: 5.5-5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0212 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2018 / Details: Sagittal focusing 2nd crystal horizontal focusing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0212 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→33.15 Å / Num. obs: 45669 / % possible obs: 99.2 % / Redundancy: 3.68 % / Biso Wilson estimate: 11.9 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.42 / Net I/σ(I): 24.44 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XU9 Resolution: 1.702→33.149 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.64 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.23 Å2 / Biso mean: 16.8935 Å2 / Biso min: 1.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.702→33.149 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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