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- PDB-1pul: Solution structure for the 21KDa caenorhabditis elegans protein C... -

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Basic information

Entry
Database: PDB / ID: 1pul
TitleSolution structure for the 21KDa caenorhabditis elegans protein CE32E8.3. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET WR33
ComponentsHypothetical protein C32E8.3 in chromosome IHypothesis
Keywordsstructural genomics / unknown function / ALPHA HELICAL / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / PSI / Protein Structure Initiative / NESG
Function / homologyP25-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 speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTejero, 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)
CitationJournal: 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
DepositionJun 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein C32E8.3 in chromosome I


Theoretical massNumber of molelcules
Total (without water)13,7481
Polymers13,7481
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 56target function
Representative

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Components

#1: Protein Hypothetical protein C32E8.3 in chromosome I / Hypothesis


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-NOESY
1213D 13C-NOESY
1312D 15N,1H HSQC
NMR detailsText: 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.

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Sample preparation

DetailsContents: 1mM WR33 U-15N,13C; 20mM NaH2PO4, 50mM NaCl, 10mM DTT, 0.02% azide
Solvent system: 95% H20, 5% D2O, PH 6.5
Sample conditionsIonic strength: 50 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Bcollection
NMRPipe2.1processing
Sparky3.106data analysis
AutoAssign1.11.0data analysis
TALOS2.1data analysis
DYANA1.5Guntertrefinement
AutoStructure2.1.0Huang, Montelionerefinement
CNS1.1Brungerrefinement
PSVS1Bhattacharya, Montelionedata analysis
RefinementMethod: 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 ensembleConformer selection criteria: target function / Conformers calculated total number: 56 / Conformers submitted total number: 10

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