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- PDB-1sgo: NMR Structure of the human C14orf129 gene product, HSPC210. North... -

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Basic information

Entry
Database: PDB / ID: 1sgo
TitleNMR Structure of the human C14orf129 gene product, HSPC210. Northeast Structural Genomics target HR969.
ComponentsProtein C14orf129
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HR969 / HUMAN PROTEIN / NESG / Hs.4104 homo sapiens / NESG cluster ID 18152. / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


kinase regulator activity / regulation of Wnt signaling pathway / intrinsic apoptotic signaling pathway in response to oxidative stress / protein kinase A binding / protein kinase A regulatory subunit binding / protein kinase inhibitor activity / negative regulation of protein kinase activity / positive regulation of canonical Wnt signaling pathway / protein kinase binding / nucleus / cytoplasm
Similarity search - Function
copper amine oxidase-like fold / Hypothetical protein (hspc210) / GSKIP domain / GSK3B-interacting protein / GSKIP domain / GSKIP domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GSK3B-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS
AuthorsRamelot, T.A. / Cort, J.R. / Xiao, R. / Shih, L.-Y. / Ma, L.-C. / Acton, T.B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Structure of the human C14orf129 gene product, HSPC210. Northeast Structural Genomics target HR969.
Authors: Ramelot, T.A. / Cort, J.R. / Xiao, R. / Shih, L.-Y. / Ma, L.-C. / Acton, T.B. / Montelione, G.T. / Kennedy, M.A.
History
DepositionFeb 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: Protein C14orf129


Theoretical massNumber of molelcules
Total (without water)15,6621
Polymers15,6621
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 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein C14orf129 / HSPC210


Mass: 15662.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C14ORF129 / Plasmid: PET14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(LAMDA DE3)PMGK / References: UniProt: Q9P0R6

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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
1424D 13C-separated NOESY
15313C HSQC
161H/D EXCHANGE

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM HSPC210, U-15N, 13C; 20 mM MES, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02% NaN395% H2O/5% D2O
21mM HSPC210, U-15N, 13C; 20 mM MES, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02% NaN3100% D2O
31mM HSPC210, U-15N, 5%-13C; 20 mM MES, 100 mM NaCl, 10 mM DTT, 5 mM CaCl2, 0.02% NaN395% H2O/5% D2O
Sample conditionsIonic strength: 100mM 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 UNITYVarianUNITY6003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.98T.D. GODDARD, D.G. KNELLERdata analysis
Felix98MSI (ACCELRYS)processing
AutoStructure1.1.2Y.J. HUANG, G.T. MONTELIONEdata analysis
TALOS199.019.15.27G. CORNILESCU, F. DELAGLIO, A. BAXdata analysis
X-PLORXPLOR-NIH-2.0.6C.D. SCHWIETERS, J.J. KUSZEWSKI, N. TJANDRA, G.M. CLOREstructure solution
CNS1.1A. BRUNGERrefinement
VNMR6.1cVariancollection
RefinementMethod: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1132 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE RESTRAINTS: TOTAL = 1000; INTRA-RESIDUE [I=J] = 23; SEQUENTIAL [(I-J)=1] = 239; MEDIUM ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1132 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE RESTRAINTS: TOTAL = 1000; INTRA-RESIDUE [I=J] = 23; SEQUENTIAL [(I-J)=1] = 239; MEDIUM RANGE [1<(I-J)<5] = 304; LONG RANGE [(I-J)>=5] = 382; HYDROGEN BOND RESTRAINTS = 52 (2 PER H-BOND); NUMBER OF DISTANCE RESTRAINTS PER RESIDUE = 9.7 (RESIDES 33-135); DIHEDRAL-ANGLE RESTRAINTS = 132 (66 PHI, 66 PSI); TOTAL NUMBER OF RESTRAINTS PER RESIDUE = 10.3 (RESIDES 33-135); NUMBER OF LONG RANGE RESTRA NTS PER RESIDUE = 3.7; NUMBER OF STRUCTURES COMPUTED = 20; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.1 ANG = 2.3; AVERAGE R.M.S. DISTANCE VIOLATION = 0.011 ANG; MAXIMUM NUMBER OF DISTANCE VIOLATIONS 4. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >1 DEG = 1.5; MAX NUMBER OF DIHEDRAL ANGLE VIOLATIONS = 4; AVERAGE R.M.S. ANGLE VIOLATION = 0.17 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C',O, RESIDUES 33-135) = 0.67 ANG; ALL HEAVY ATOMS = 1.21 ANG; PROCHECK (RESDIUES 31-135): MOST FAVORED EGIONS = 86%; ADDITIONAL ALLOWED REGIONS = 13%; GENEROUSLY ALLOWED REGIONS = 1%; DISALLOWED REGIONS = 0%. THE UNSTRUCTURED 10 RESIDUE N-TERMINAL HIS TAG (MGHHHHHHSH) WAS NOT INCLUDED IN THE STRUCTURE CALCULATION.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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