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- PDB-1um1: Solution Structure of RSGI RUH-007, PDZ domain in Human cDNA -

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Basic information

Entry
Database: PDB / ID: 1um1
TitleSolution Structure of RSGI RUH-007, PDZ domain in Human cDNA
ComponentsKIAA1849 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PDZ domain / Human cDNA / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


substrate adhesion-dependent cell spreading / microtubule / multicellular organism development / signal transduction / protein-containing complex
Ubiquitin-like domain superfamily / DIL domain / Dilute domain profile. / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / PDZ domain / Dilute domain / SMAD/FHA domain superfamily / PDZ domain profile. / PDZ superfamily ...Ubiquitin-like domain superfamily / DIL domain / Dilute domain profile. / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / PDZ domain / Dilute domain / SMAD/FHA domain superfamily / PDZ domain profile. / PDZ superfamily / Rasip1/Radil, cargo-binding domain / PDZ domain / Ras association (RalGDS/AF-6) domain
Ras-associating and dilute domain-containing protein
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDoi-Katayama, Y. / Hayashi, F. / Hirota, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of RSGI RUH-007, a PDZ Domain in Human cDNA
Authors: Doi-Katayama, Y. / Hayashi, F. / Hirota, H. / Yokoyama, S.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 22, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KIAA1849 protein


Theoretical massNumber of molelcules
Total (without water)11,3031
Polymers11,3031
Non-polymers00
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide KIAA1849 protein / RSGI RUH-007


Mass: 11302.925 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: Kazusa cDNA KIAA1849 / Plasmid: P021030-50 / References: UniProt: Q96JH8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment

Conditions-ID: 1 / Solution-ID: 1

Experiment-IDType
13D 13C-separated NOESY
23D 15N-separated NOESY

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Sample preparation

DetailsContents: 0.7mM PDZ domain U-15N, 13C; 20mM Tris-HCl (pH 7.0); 100mM NaCl; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
Kujira0.816Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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