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Yorodumi- PDB-1sgo: NMR Structure of the human C14orf129 gene product, HSPC210. North... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sgo | ||||||
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Title | NMR Structure of the human C14orf129 gene product, HSPC210. Northeast Structural Genomics target HR969. | ||||||
Components | Protein C14orf129 | ||||||
Keywords | STRUCTURAL 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 / protein kinase A binding / intrinsic apoptotic signaling pathway in response to oxidative stress / protein kinase inhibitor activity / protein kinase A regulatory subunit binding / negative regulation of protein kinase activity / positive regulation of canonical Wnt signaling pathway / protein kinase binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS | ||||||
Authors | Ramelot, 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) | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sgo.cif.gz | 826.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sgo.ent.gz | 696.4 KB | Display | PDB format |
PDBx/mmJSON format | 1sgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sgo_validation.pdf.gz | 342.7 KB | Display | wwPDB validaton report |
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Full document | 1sgo_full_validation.pdf.gz | 472.5 KB | Display | |
Data in XML | 1sgo_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 1sgo_validation.cif.gz | 69.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/1sgo ftp://data.pdbj.org/pub/pdb/validation_reports/sg/1sgo | 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: 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 100mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 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: 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 20 |