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Yorodumi- PDB-1pul: Solution structure for the 21KDa caenorhabditis elegans protein C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pul | ||||||
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Title | Solution structure for the 21KDa caenorhabditis elegans protein CE32E8.3. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET WR33 | ||||||
Components | Hypothetical protein C32E8.3 in chromosome I | ||||||
Keywords | structural genomics / unknown function / ALPHA HELICAL / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / PSI / Protein Structure Initiative / NESG | ||||||
Function / homology | P25-alpha / p25-alpha / positive regulation of protein polymerization / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha / Tubulin polymerization-promoting protein homolog Function and homology information | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Tejero, R. / Aramini, J.M. / Swapna, G.V.T. / Monleon, D. / Chiang, Y. / Macapagal, D. / Gunsalus, K.C. / Kim, S. / Szyperski, T. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: J.Biomol.Nmr / Year: 2004 Title: Backbone 1H, 15N and 13C assignments for the 21 kDa Caenorhabditis elegans homologue of "brain-specific" protein. Authors: Monleon, D. / Chiang, Y. / Aramini, J.M. / Swapna, G.V. / Macapagal, D. / Gunsalus, K.C. / Kim, S. / Szyperski, T. / Montelione, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pul.cif.gz | 323.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pul.ent.gz | 266.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pul_validation.pdf.gz | 345.1 KB | Display | wwPDB validaton report |
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Full document | 1pul_full_validation.pdf.gz | 425.2 KB | Display | |
Data in XML | 1pul_validation.xml.gz | 19 KB | Display | |
Data in CIF | 1pul_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/1pul ftp://data.pdbj.org/pub/pdb/validation_reports/pu/1pul | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13747.630 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: C32E8.3 / Plasmid details: derivative of pET15b / Plasmid: pET15b-WR33 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P91127 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN. MANUAL SIDE CHAIN ASSIGNMENTS. AUTOMATIC NOESY ASSIGNMENTS AS ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN. MANUAL SIDE CHAIN ASSIGNMENTS. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING HYPER AND TALOS. FINAL STRUCTURE QUALITY FACTORS FOR THE ENSEMBLE (RESIDUES 18 to 120), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 19-33,42-56,61-62,64-74,77-79,83-119: (A) RMSD FOR ORDERED RESIDUES: BB, 1.2; HEAVY ATOM, 1.7 (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED: 93.0%; ADDITIONALLY ALLOWED: 5.7%; GENEROUSLY ALLOWED, 0.8%; DISALLOWED, 0.5% (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): BB, 0.20/1.10; ALL, -0.02/-0.12. (D) MAGE MOLPROBITY CLASH SCORE (RAW/Z-): 33.54/-4.23. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA: F-MEASURE, 0.834; RECALL, 0.900; PRECISION, 0.776; DP-SCORE, 0.606. |
-Sample preparation
Details | Contents: 1mM WR33 U-15N,13C; 20mM NaH2PO4, 50mM NaCl, 10mM DTT, 0.02% azide Solvent system: 95% H20, 5% D2O, PH 6.5 |
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Sample conditions | Ionic strength: 50 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON A TOTAL 729 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 260 DIHEDRAL ANGLE CONSTRAINTS, AND 50 HYDROGEN BOND CONSTRAINTS (9.3 CONSTRAINTS PER ...Details: THE STRUCTURES ARE BASED ON A TOTAL 729 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 260 DIHEDRAL ANGLE CONSTRAINTS, AND 50 HYDROGEN BOND CONSTRAINTS (9.3 CONSTRAINTS PER RESIDUE; 1.2 LONG-RANGE CONSTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (DYANA). THE 10 STRUCTURES WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE UNSTRUCTURED N- (1 to 17) AND C- (121 to 125) TERMINAL REGIONS OF THE MOLECULE ARE OMITTED FROM THIS DEPOSITION. | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 56 / Conformers submitted total number: 10 |