+Open data
-Basic information
Entry | Database: PDB / ID: 3a57 | ||||||
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Title | Crystal structure of Thermostable Direct Hemolysin | ||||||
Components | Thermostable direct hemolysin 2 | ||||||
Keywords | TOXIN / hemolysin / Cytolysis / Disulfide bond / Hemolysis | ||||||
Function / homology | Function and homology information hemolysis by symbiont of host erythrocytes / : / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Vibrio parahaemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å | ||||||
Authors | Hashimoto, H. / Yanagihara, I. / Nakahira, K. / Hamada, D. / Ikegami, T. / Mayanagi, K. / Kaieda, S. / Fukui, T. / Ohnishi, K. / Kajiyama, S. ...Hashimoto, H. / Yanagihara, I. / Nakahira, K. / Hamada, D. / Ikegami, T. / Mayanagi, K. / Kaieda, S. / Fukui, T. / Ohnishi, K. / Kajiyama, S. / Yamane, T. / Ikeguchi, M. / Honda, T. / Shimizu, T. / Sato, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin Authors: Yanagihara, I. / Nakahira, K. / Yamane, T. / Kaieda, S. / Mayanagi, K. / Hamada, D. / Fukui, T. / Ohnishi, K. / Kajiyama, S. / Shimizu, T. / Sato, M. / Ikegami, T. / Ikeguchi, M. / Honda, T. / Hashimoto, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a57.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a57.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 3a57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a57_validation.pdf.gz | 421.4 KB | Display | wwPDB validaton report |
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Full document | 3a57_full_validation.pdf.gz | 422.6 KB | Display | |
Data in XML | 3a57_validation.xml.gz | 10 KB | Display | |
Data in CIF | 3a57_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/3a57 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/3a57 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18659.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: tdh / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P19250 |
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#2: Water | ChemComp-HOH / |
Sequence details | SEE REFERENCE 1 AND 4 IN UNP DATABASE P19250 (HLY2_VIBPA) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.6 Details: Lithium sulfate, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.5→50 Å / Num. obs: 25349 / % possible obs: 97.5 % / Rmerge(I) obs: 0.046 | |||||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.28 / % possible all: 79.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.047 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.064 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.607 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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