+
Open data
-
Basic information
Entry | Database: PDB / ID: 2hqx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human P100 tudor domain conserved region | ||||||
![]() | P100 CO-ACTIVATOR TUDOR DOMAIN | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() regulation of cell cycle process / miRNA catabolic process / RISC complex binding / dense body / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhao, M. / Liu, Z.J. / Xu, H. / Yang, J. / Silvennoinen, O. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
![]() | ![]() Title: Crystal Structure of Human P100 Tudor Domain Conserved Region Authors: Zhao, M. / Liu, Z.J. / Xu, H. / Yang, J. / Silvennoinen, O. / Wang, B.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 58.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 38.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2hqeS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | THE INTACT P100 PROTEIN ASSOCIATES AS A DIMER |
-
Components
#1: Protein | Mass: 27941.320 Da / Num. of mol.: 2 / Fragment: CONSERVED REGION Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal grow![]() | Temperature: 291 K / Method: modified microbatch / pH: 7.9 Details: 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (11.0 MG/ML) AND RESERVOIR SOLUTION CONTAINING 1.06M AMMONIUM SULFATE, 200.0 MM LITHIUM SULFATE, 0.1M TRIS PH 7.9, ...Details: 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (11.0 MG/ML) AND RESERVOIR SOLUTION CONTAINING 1.06M AMMONIUM SULFATE, 200.0 MM LITHIUM SULFATE, 0.1M TRIS PH 7.9, MODIFIED MICROBATCH, temperature 291K |
---|
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 25, 2005 / Details: ROSENBAUM | |||||||||
Radiation | Monochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.42→38.72 Å / Num. all: 27043 / Num. obs: 25303 / % possible obs: 82.17 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.05 / Net I/σ(I): 15.6 | |||||||||
Reflection shell | Resolution: 1.42→1.46 Å / Redundancy: 1.3 % / Num. unique all: 212 / Rsym value: 0.03 / % possible all: 23.08 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() Starting model: PDB ENTRY 2HQE Resolution: 1.42→38.72 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / SU B: 1.608 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.11 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→38.72 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.42→1.456 Å / Total num. of bins used: 20
|