- PDB-2ypd: Crystal structure of the Jumonji domain of human Jumonji domain c... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2ypd
Title
Crystal structure of the Jumonji domain of human Jumonji domain containing 1C protein
Components
PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN 2C
Keywords
OXIDOREDUCTASE
Function / homology
Function and homology information
Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / nuclear thyroid hormone receptor binding / dioxygenase activity / histone H3K9 demethylase activity / histone deacetylase complex / transcription coregulator activity / chromatin DNA binding / blood coagulation / Factors involved in megakaryocyte development and platelet production / chromatin ...Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / nuclear thyroid hormone receptor binding / dioxygenase activity / histone H3K9 demethylase activity / histone deacetylase complex / transcription coregulator activity / chromatin DNA binding / blood coagulation / Factors involved in megakaryocyte development and platelet production / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding Similarity search - Function
Histone demethylase JHDM2-like / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology
PROBABLEJMJCDOMAIN-CONTAININGHISTONEDEMETHYLATIONPROTEIN2C / JUMONJI DOMAIN-CONTAINING PROTEIN 1C / THYROID RECEPTOR-INTERACTING PROTEIN 8 / TR-INTERACTING ...JUMONJI DOMAIN-CONTAINING PROTEIN 1C / THYROID RECEPTOR-INTERACTING PROTEIN 8 / TR-INTERACTING PROTEIN 8 / TRIP-8
Mass: 45190.605 Da / Num. of mol.: 2 / Fragment: JUMONJI DOMAIN, RESIDUES 2157-2540 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: Q15652, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9736 Å / Relative weight: 1
Reflection
Resolution: 2.1→92.82 Å / Num. obs: 50717 / % possible obs: 100 % / Observed criterion σ(I): 1.7 / Redundancy: 15.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.5
Reflection shell
Resolution: 2.1→2.16 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.7 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.7.0029
refinement
MOSFLM
datareduction
SCALA
datascaling
autoSHARP
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 2.1→92.82 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.356 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23986
2574
5.1 %
RANDOM
Rwork
0.2149
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obs
0.21616
48077
99.97 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK