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Yorodumi- PDB-4q8b: The crystal structure of CotA laccase complexed with sinapic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q8b | ||||||
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Title | The crystal structure of CotA laccase complexed with sinapic acid | ||||||
Components | Spore coat protein A | ||||||
Keywords | OXIDOREDUCTASE / Laccase / Sinapic acid | ||||||
Function / homology | Function and homology information bilirubin oxidase / laccase / sporulation resulting in formation of a cellular spore / outer membrane-bounded periplasmic space / oxidoreductase activity / copper ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Xie, T. / Liu, Z.C. / Wang, G.G. | ||||||
Citation | Journal: To be Published Title: The crystal structure of CotA laccase complexed with sinapic acid Authors: Xie, T. / Liu, Z.C. / Wang, G.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q8b.cif.gz | 233.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q8b.ent.gz | 183.5 KB | Display | PDB format |
PDBx/mmJSON format | 4q8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q8b_validation.pdf.gz | 457.6 KB | Display | wwPDB validaton report |
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Full document | 4q8b_full_validation.pdf.gz | 459.6 KB | Display | |
Data in XML | 4q8b_validation.xml.gz | 44.6 KB | Display | |
Data in CIF | 4q8b_validation.cif.gz | 68.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/4q8b ftp://data.pdbj.org/pub/pdb/validation_reports/q8/4q8b | HTTPS FTP |
-Related structure data
Related structure data | 4q89C 1gskS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 2 - 511 / Label seq-ID: 2 - 511
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 58574.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Strain: 168 / Gene: cotA, pig, BSU06300 / Production host: Escherichia coli (E. coli) / References: UniProt: P07788 |
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-Non-polymers , 7 types, 921 molecules
#2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-OXY / | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-SXX / | #7: Chemical | ChemComp-PGE / | #8: 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: 2.12 Å3/Da / Density % sol: 42.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12-15.5% PEG3350, 0.1M MgCl2, 0.1M pH 6.5 Bis-tris, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→29.81 Å / Num. all: 75023 / Num. obs: 71222 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GSK Resolution: 1.91→29.81 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.812 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY THE COPPER ATOMS WITH THE ANISOU RECORD WERE REFINED ANISOTROPICALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.903 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→29.81 Å
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Refine LS restraints |
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