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Yorodumi- PDB-6uts: Crystal Structure of bacterial pirin YhhW in complex with nickel(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uts | ||||||
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Title | Crystal Structure of bacterial pirin YhhW in complex with nickel(II) from Escherichia coli | ||||||
Components | Quercetin 2,3-dioxygenase | ||||||
Keywords | METAL BINDING PROTEIN / bacterial pirin / nickel binding / quercetinase / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / dioxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å | ||||||
Authors | Guo, B. / Zhang, Y. / Jia, Z. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2019 Title: Structure-Dependent Modulation of Substrate Binding and Biodegradation Activity of Pirin Proteins toward Plant Flavonols. Authors: Guo, B. / Zhang, Y. / Hicks, G. / Huang, X. / Li, R. / Roy, N. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uts.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uts.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 6uts.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uts_validation.pdf.gz | 248 KB | Display | wwPDB validaton report |
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Full document | 6uts_full_validation.pdf.gz | 248 KB | Display | |
Data in XML | 6uts_validation.xml.gz | 988 B | Display | |
Data in CIF | 6uts_validation.cif.gz | 3.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/6uts ftp://data.pdbj.org/pub/pdb/validation_reports/ut/6uts | HTTPS FTP |
-Related structure data
Related structure data | 1tq5S 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
#1: Protein | Mass: 26310.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 Gene: FAM12_08410, FAM13_08105, FAZ80_08430, FAZ81_08230, FAZ83_10840, FAZ86_07885, FAZ87_06805 Production host: Escherichia coli (E. coli) / References: UniProt: A0A4S5WTB9, UniProt: P46852*PLUS |
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#2: Chemical | ChemComp-NI / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.69 Å3/Da / Density % sol: 73.8 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1 M MES (pH 6.5) and 14% (w/v) PEG 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03319 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03319 Å / Relative weight: 1 |
Reflection | Resolution: 3.088→28.39 Å / Num. obs: 9553 / % possible obs: 98.9 % / Redundancy: 25 % / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.207 / Net I/σ(I): 15.08 |
Reflection shell | Resolution: 3.088→3.102 Å / Num. unique obs: 9607 / CC1/2: 0.678 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TQ5 Resolution: 3.09→28.39 Å / SU ML: 0.4886 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1549
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 104.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.09→28.39 Å
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Refine LS restraints |
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LS refinement shell |
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