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Yorodumi- PDB-7yva: Crystal structure of Candida albicans Fructose-1,6-bisphosphate a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yva | ||||||
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Title | Crystal structure of Candida albicans Fructose-1,6-bisphosphate aldolase complexed with lipoic acid | ||||||
Components | Candida albicans Fructose-1,6-bisphosphate aldolase | ||||||
Keywords | CYTOSOLIC PROTEIN/INHIBITOR / non-covalent inhibitor / CYTOSOLIC PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host immune response / hyphal cell wall / fungal-type cell wall / fructose-bisphosphate aldolase / biological process involved in interaction with host / fructose-bisphosphate aldolase activity / gluconeogenesis / glycolytic process / cell surface / zinc ion binding ...symbiont-mediated perturbation of host immune response / hyphal cell wall / fungal-type cell wall / fructose-bisphosphate aldolase / biological process involved in interaction with host / fructose-bisphosphate aldolase activity / gluconeogenesis / glycolytic process / cell surface / zinc ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å | ||||||
Authors | Cao, H. / Huang, Y. / Ren, Y. / Wan, J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Candida albicans Fructose-1,6-bisphosphate aldolase complexed with lipoic acid Authors: Cao, H. / Huang, Y. / Ren, Y. / Wan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yva.cif.gz | 276.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yva.ent.gz | 223.6 KB | Display | PDB format |
PDBx/mmJSON format | 7yva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yva_validation.pdf.gz | 736.8 KB | Display | wwPDB validaton report |
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Full document | 7yva_full_validation.pdf.gz | 759.8 KB | Display | |
Data in XML | 7yva_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 7yva_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/7yva ftp://data.pdbj.org/pub/pdb/validation_reports/yv/7yva | HTTPS FTP |
-Related structure data
Related structure data | 6lnkS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39263.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9URB4 #2: Chemical | #3: Chemical | ChemComp-LPA / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.33 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 22.5% (w/v) PEG 3350 100 mM Hepes pH =7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.93→45.37 Å / Num. obs: 15544 / % possible obs: 98.47 % / Redundancy: 3.3 % / Biso Wilson estimate: 79.64 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.38 |
Reflection shell | Resolution: 2.93→3.04 Å / Num. unique obs: 1493 / CC1/2: 0.752 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LNK Resolution: 2.93→45.37 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 152.36 Å2 / Biso mean: 77.9798 Å2 / Biso min: 47.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.93→45.37 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Origin x: -23.2191 Å / Origin y: 1.4468 Å / Origin z: 17.3697 Å
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Refinement TLS group |
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