- PDB-4aap: Crystal structure of JMJD5 domain of human Lysine-specific demeth... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4aap
Title
Crystal structure of JMJD5 domain of human Lysine-specific demethylase 8 (KDM8) in complex with N-oxalylglycine (NOG)
Components
LYSINE-SPECIFIC DEMETHYLASE 8
Keywords
OXIDOREDUCTASE
Function / homology
Function and homology information
[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle / p53 binding / chromosome / fibroblast proliferation / endopeptidase activity / in utero embryonic development / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / proteolysis / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function
Cupin-like domain 8 / Cupin-like domain / Cupin / 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
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97 Å / Relative weight: 1
Reflection
Resolution: 2.6→19.91 Å / Num. obs: 23473 / % possible obs: 99.5 % / Observed criterion σ(I): 2.2 / Redundancy: 7 % / Biso Wilson estimate: 88.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2
Reflection shell
Resolution: 2.6→2.74 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7
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Processing
Software
Name
Version
Classification
REFMAC
5.6.0117
refinement
XDS
datareduction
SCALA
datascaling
SHARP
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 2.6→89.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 20.432 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2529
1210
5.2 %
RANDOM
Rwork
0.20766
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obs
0.20984
22281
99.61 %
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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