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Yorodumi- PDB-1lpl: Structural Genomics of Caenorhabditis elegans: CAP-Gly domain of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lpl | ||||||
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Title | Structural Genomics of Caenorhabditis elegans: CAP-Gly domain of F53F4.3 | ||||||
Components | Hypothetical 25.4 kDa protein F53F4.3 in chromosome V | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / CAP-Gly domain / cytoskeleton / tubulin / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG | ||||||
Function / homology | Function and homology information post-chaperonin tubulin folding pathway / tubulin complex assembly / alpha-tubulin binding / microtubule / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAS / Resolution: 1.77 Å | ||||||
Authors | Li, S. / Finley, J. / Liu, Z.-J. / Qiu, S.H. / Luan, C.H. / Carson, M. / Tsao, J. / Johnson, D. / Lin, G. / Zhao, J. ...Li, S. / Finley, J. / Liu, Z.-J. / Qiu, S.H. / Luan, C.H. / Carson, M. / Tsao, J. / Johnson, D. / Lin, G. / Zhao, J. / Thomas, W. / Nagy, L.A. / Sha, B. / DeLucas, L.J. / Wang, B.-C. / Luo, M. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal Structure of the Cytoskeleton-associated Protein Glycine-rich (CAP-Gly) Domain Authors: Li, S. / Finley, J. / Liu, Z.-J. / Qiu, S.H. / Luan, C.H. / Carson, M. / Tsao, J. / Johnson, D. / Lin, G. / Zhao, J. / Thomas, W. / Nagy, L.A. / Sha, B. / DeLucas, L.J. / Wang, B.-C. / Luo, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lpl.cif.gz | 31.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lpl.ent.gz | 21.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lpl_validation.pdf.gz | 415.5 KB | Display | wwPDB validaton report |
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Full document | 1lpl_full_validation.pdf.gz | 417.2 KB | Display | |
Data in XML | 1lpl_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 1lpl_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/1lpl ftp://data.pdbj.org/pub/pdb/validation_reports/lp/1lpl | 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: 10358.670 Da / Num. of mol.: 1 / Fragment: CAP-Gly domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: F53F4.3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q20728 |
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#2: 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: 2.92 Å3/Da / Density % sol: 57.91 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Reservoir solution contained 1.8 M ammonium sulphate and 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / 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: APS / Beamline: 17-ID / Wavelength: 1.74 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 10, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.74 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. all: 12627 / Num. obs: 12627 / % possible obs: 100 % / Observed criterion σ(F): 0.001 / Observed criterion σ(I): 0.001 / Biso Wilson estimate: 23.3 Å2 |
Reflection shell | Resolution: 1.77→1.88 Å / % possible all: 91.9 |
Reflection | *PLUS Num. obs: 12651 / % possible obs: 99.2 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS % possible obs: 95 % / Rmerge(I) obs: 0.369 |
-Processing
Software |
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Refinement | Method to determine structure: SAS / Resolution: 1.77→30.6 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 29.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.77→30.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.88 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor obs: 0.225 / Rfactor Rfree: 0.294 / Rfactor Rwork: 0.225 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.365 |