+
Open data
-
Basic information
Entry | Database: PDB / ID: 4o64 | ||||||
---|---|---|---|---|---|---|---|
Title | Zinc fingers of KDM2B | ||||||
![]() | Lysine-specific demethylase 2B | ||||||
![]() | METAL BINDING PROTEIN / CXXC zinc finger / ring zinc finger / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() initiation of neural tube closure / fourth ventricle development / midbrain-hindbrain boundary morphogenesis / third ventricle development / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / embryonic camera-type eye morphogenesis / lateral ventricle development / negative regulation of neural precursor cell proliferation / hindbrain development ...initiation of neural tube closure / fourth ventricle development / midbrain-hindbrain boundary morphogenesis / third ventricle development / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / embryonic camera-type eye morphogenesis / lateral ventricle development / negative regulation of neural precursor cell proliferation / hindbrain development / PcG protein complex / unmethylated CpG binding / histone H3K36 demethylase activity / midbrain development / positive regulation of stem cell population maintenance / histone demethylase activity / forebrain development / transcription coregulator activity / HDMs demethylate histones / chromosome / positive regulation of cell growth / spermatogenesis / negative regulation of neuron apoptotic process / rRNA binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, K. / Xu, C. / Tempel, W. / Walker, J.R. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants. Authors: Xu, C. / Liu, K. / Lei, M. / Yang, A. / Li, Y. / Hughes, T.R. / Min, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 150.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 118.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4nw3C ![]() 4pziC ![]() 4z3cC ![]() 5vc9C ![]() 5w9qC ![]() 5w9sC ![]() 6asbC ![]() 6asdC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 13350.738 Da / Num. of mol.: 3 / Fragment: UNP Residues 607-723 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.3 % |
---|---|
Crystal grow | Temperature: 291 K / Method: sitting drop / pH: 8.5 Details: 25% PEG 8000, 0.2 M sodium chloride, 0.1 M tris, pH 8.5, sitting drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2013 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.28315 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.13→46.47 Å / Num. obs: 24576 / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 12.5 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 5.7 %
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: arp/warp was used for automated model building. coot was used for interactive model building. Model geometry was assessed on the molprobity server.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.26 Å2 / Biso mean: 37.3248 Å2 / Biso min: 14.28 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→40 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.13→2.185 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|