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- PDB-2jve: Solution structure of the extracellular domain of Prod1, a protei... -

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Basic information

Entry
Database: PDB / ID: 2jve
TitleSolution structure of the extracellular domain of Prod1, a protein implicated in proximodistal identity during amphibian limb regeneration
ComponentsProd 1
KeywordsTOXIN / Ly-6 / three-finger snake toxin / UPAR / CD59 / Limb regeneration
Function / homologyCD59 / CD59 / Ribbon / Mainly Beta / Prod 1
Function and homology information
Biological speciesNotophthalmus viridescens (eastern newt)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsGarza-Garcia, A. / Harris, R. / Esposito, D. / Driscoll, P.C.
CitationJournal: Plos One / Year: 2009
Title: Solution structure and phylogenetics of Prod1, a member of the three-finger protein superfamily implicated in salamander limb regeneration.
Authors: Garza-Garcia, A. / Harris, R. / Esposito, D. / Gates, P.B. / Driscoll, P.C.
History
DepositionSep 19, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 19, 2012Group: Database references / Source and taxonomy
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Remark 999Sequence The sequence is not available at UniProt database at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prod 1


Theoretical massNumber of molelcules
Total (without water)10,2241
Polymers10,2241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Prod 1


Mass: 10223.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Notophthalmus viridescens (eastern newt)
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8D0E6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1313D 1H-15N NOESY
1433D 1H-13C NOESY
1533D 1H-13C aromatic NOESY
1623D CBCA(CO)NH
1723D HNCO
1823D HNCA
1923D HN(CA)CB
11023D HN(CO)CA
11123D HN(CA)CO
11223D HA(CA)NH
11323D HN(CACO)NH
11433D (H)CCH-TOCSY
11533D (H)CCH-COSY
11613D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-13C; U-15N] Prod1, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMProd1[U-15N]1
50 mMsodium phosphate1
150 mMsodium chloride1
1 mMEDTA1
1 mMProd1[U-13C; U-15N]2
50 mMsodium phosphate2
150 mMsodium chloride2
1 mMEDTA2
1 mMProd1[U-13C; U-15N]3
50 mMsodium phosphate3
150 mMsodium chloride3
1 mMEDTA3
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003
Varian UnityPlusVarianUNITYPLUS5004

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, F. et al.processing
ANSIGKraulis, P.J.data analysis
X-PLOR NIHSchwieters, C.D. et al.refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: the structures were calculated using an ab-initio simulated annealing protocol within the CNS/Xplor-NIH programs with PARALLHDG v5.3 parameter set and PROLSQ non-bonded energy function. ...Details: the structures were calculated using an ab-initio simulated annealing protocol within the CNS/Xplor-NIH programs with PARALLHDG v5.3 parameter set and PROLSQ non-bonded energy function. Cartesian and torsion angle dynamics were used to refine the structures.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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