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- PDB-1xpw: Solution NMR Structure of human protein HSPCO34. Northeast Struct... -

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Basic information

Entry
Database: PDB / ID: 1xpw
TitleSolution NMR Structure of human protein HSPCO34. Northeast Structural Genomics Target HR1958
ComponentsLOC51668 protein
KeywordsStructural Genomics / Unknown Function / gene PP25 / locus LOC51668 / C1orf41 / homo sapiens / NESGC cluster id 3237 / target HR1958 / APC10-related protein / Northeast Structural Genomics Consortium / protein structure initiative / PSI / jellyroll / Beta-sandwich
Function / homology
Function and homology information


intraciliary anterograde transport / intraciliary transport particle B / left/right axis specification / ciliary tip / Intraflagellar transport / smoothened signaling pathway / cilium assembly / kidney development / skeletal system development / lung development ...intraciliary anterograde transport / intraciliary transport particle B / left/right axis specification / ciliary tip / Intraflagellar transport / smoothened signaling pathway / cilium assembly / kidney development / skeletal system development / lung development / cilium / protein transport / heart development / spermatogenesis / cell differentiation / centrosome / metal ion binding
Similarity search - Function
Intraflagellar transport protein 25 / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Intraflagellar transport protein 25 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / XPLOR SIMULATED ANNEALING, CNS WATER REFINEMENT
AuthorsRamelot, T.A. / Xiao, R. / Ma, L.C. / Acton, T.B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2009
Title: Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.
Authors: Ramelot, T.A. / Raman, S. / Kuzin, A.P. / Xiao, R. / Ma, L.C. / Acton, T.B. / Hunt, J.F. / Montelione, G.T. / Baker, D. / Kennedy, M.A.
History
DepositionOct 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 400COMPOUND THIS PROTEIN HAS STOICHIOMETRIC CALCIUM BOUND. CALCIUM COORDINATION COULD NOT BE ...COMPOUND THIS PROTEIN HAS STOICHIOMETRIC CALCIUM BOUND. CALCIUM COORDINATION COULD NOT BE DETERMINED, BUT IS CONSISTENT WITH PDB ENTRY 1TVG

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LOC51668 protein


Theoretical massNumber of molelcules
Total (without water)17,4431
Polymers17,4431
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)20 / 25structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein LOC51668 protein / HSPC034


Mass: 17442.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PP25 / Plasmid: PET14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (LAMDA DE3) PMGK / References: UniProt: Q9Y547

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
14213C HSQC
1534D 13C-separated NOESY
163H/D exchange

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM U-15N,13C protein, 20 mM MES, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02% NaN3, 95% H2O, 5% D2O95% H2O/5% D2O
21 mM U-15N,13C protein, 20 mM MES, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02% NaN3, 100% D2O100% D2O
31 mM U-15N,5%-13C protein, 20 mM MES, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02% NaN3, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 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 INOVAVarianINOVA8001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003
Varian UNITYVarianUNITY6004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipenmrpipe.linuxDelaglioprocessing
Felix98Accelrysprocessing
AutoStructure2.1.0Y.J. Huang, G.T. Montelionedata analysis
X-PLORXPLOR-NIH-2.0.6C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M. Clorestructure solution
CNS1.1Brungerrefinement
Sparky3.106T. Goddard, UCSFdata analysis
RefinementMethod: XPLOR SIMULATED ANNEALING, CNS WATER REFINEMENT / Software ordinal: 1
Details: The unstructured 10 residue N-terminal His tag (MGHHHHHHSH) was not included in the structure calculation.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 25 / Conformers submitted total number: 20

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