[English] 日本語
Yorodumi- PDB-2equ: Solution structure of the tudor domain of PHD finger protein 20-like 1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2equ | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the tudor domain of PHD finger protein 20-like 1 | ||||||
Components | PHD finger protein 20-like 1 | ||||||
Keywords | PROTEIN BINDING / tudor domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information methylation-dependent protein binding / NSL complex / Formation of WDR5-containing histone-modifying complexes / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein catabolic process / regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dyanamics, simulated annealing | ||||||
Authors | Futami, K. / Suzuki, S. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the tudor domain of PHD finger protein 20-like 1 Authors: Futami, K. / Suzuki, S. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2equ.cif.gz | 452.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2equ.ent.gz | 378.4 KB | Display | PDB format |
PDBx/mmJSON format | 2equ.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2equ_validation.pdf.gz | 347.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2equ_full_validation.pdf.gz | 436.4 KB | Display | |
Data in XML | 2equ_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 2equ_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/2equ ftp://data.pdbj.org/pub/pdb/validation_reports/eq/2equ | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 8315.499 Da / Num. of mol.: 1 / Fragment: tudor domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PHF20L1 / Plasmid: P060911-17 / Production host: Cell-free protein synthesis / References: UniProt: Q96BT0, UniProt: A8MW92*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.17mM 13C-15N PROTEIN; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
---|---|
Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dyanamics, simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer 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 |