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Yorodumi- PDB-1o8v: The crystal structure of Echinococcus granulosus fatty-acid-bindi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o8v | ||||||
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Title | The crystal structure of Echinococcus granulosus fatty-acid-binding protein 1 | ||||||
Components | FATTY ACID BINDING PROTEIN HOMOLOG | ||||||
Keywords | LIPID BINDING PROTEIN / FATTY-ACID-BINDING PROTEIN / ECHINOCOCCUS GRANULOSUS / HYDATID DISEASE / FATTY-ACID TRANSPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ECHINOCOCCUS GRANULOSUS (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Jakobsson, E. / Alvite, G. / Bergfors, T. / Esteves, A. / Kleywegt, G.J. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2003 Title: The Crystal Structure of Echinococcus Granulosus Fatty-Acid-Binding Protein 1 Authors: Jakobsson, E. / Alvite, G. / Bergfors, T. / Esteves, A. / Kleywegt, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o8v.cif.gz | 44.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o8v.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 1o8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o8v_validation.pdf.gz | 655.1 KB | Display | wwPDB validaton report |
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Full document | 1o8v_full_validation.pdf.gz | 655.3 KB | Display | |
Data in XML | 1o8v_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1o8v_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/1o8v ftp://data.pdbj.org/pub/pdb/validation_reports/o8/1o8v | HTTPS FTP |
-Related structure data
Related structure data | 1pmpS 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: 15131.490 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ACETYLATED AMINO TERMINUS, MODIFIED CYSTEINE A 63 / Source: (gene. exp.) ECHINOCOCCUS GRANULOSUS (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02970 | ||
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#2: Chemical | ChemComp-PLM / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | MEMBER OF THE FABP/P2/CRBP/CRABP FAMILY OF TRANSPORTEHas 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: 2 Å3/Da / Density % sol: 37.5 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.6 Details: 30% (V/V) MMEPEG 5000, 0.1 M TRIS-HCL,PH 8.6,0.1 M NAAC. | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.3 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0038 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2001 / Details: CYLINDRICAL GRAZING INCIDENCE MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0038 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 15644 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.23 % / Biso Wilson estimate: 12.69 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 35 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 14.7 / % possible all: 98.6 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 38.1 Å / Num. measured all: 81862 / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS % possible obs: 98.6 % / Rmerge(I) obs: 0.066 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PMP CHAIN A Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.171 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE LAST REFINEMENT ROUND WAS DONE AGAINST ALL DATA, RFREE VALUES ARE THE LAST RECORDED
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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: 11.29 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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