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Yorodumi- PDB-5zbf: Crystal structure of 4-hydroxyphenylpyruvic acid bound AerE from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zbf | |||||||||
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Title | Crystal structure of 4-hydroxyphenylpyruvic acid bound AerE from Microcystis aeruginosa | |||||||||
Components | Cupin domain protein | |||||||||
Keywords | ISOMERASE / Microcystis aeruginosa / Choi moiety of aeruginosins / cupin superfamily enzyme | |||||||||
Function / homology | Function and homology information Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology | |||||||||
Biological species | Microcystis aeruginosa DIANCHI905 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Qiu, X. / Zhu, W. | |||||||||
Funding support | China, 2items
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Citation | Journal: J. Struct. Biol. / Year: 2019 Title: Structural and functional insights into the role of a cupin superfamily isomerase in the biosynthesis of Choi moiety of aeruginosin. Authors: Qiu, X. / Zhu, W. / Wang, W. / Jin, H. / Zhu, P. / Zhuang, R. / Yan, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zbf.cif.gz | 107.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zbf.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 5zbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zbf_validation.pdf.gz | 437.8 KB | Display | wwPDB validaton report |
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Full document | 5zbf_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | 5zbf_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 5zbf_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/5zbf ftp://data.pdbj.org/pub/pdb/validation_reports/zb/5zbf | HTTPS FTP |
-Related 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: 24536.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microcystis aeruginosa DIANCHI905 (bacteria) Gene: aerE, C789_497 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: L8NZJ8 |
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#2: Chemical | ChemComp-ENO / |
#3: Chemical | ChemComp-FE2 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.84 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium acetate, 0.1M MES monohydrate pH 6.5, 22%(w/v) PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97923 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→45 Å / Num. obs: 27973 / % possible obs: 99 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.041 / Net I/σ(I): 22.642 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 7 % / Rmerge(I) obs: 0.911 / Mean I/σ(I) obs: 3.165 / Num. unique obs: 1335 / Rpim(I) all: 0.367 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.963 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 28.83 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→45 Å
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Refine LS restraints |
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