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Yorodumi- PDB-3kva: Structure of KIAA1718 Jumonji domain in complex with alpha-ketogl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kva | ||||||
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Title | Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate | ||||||
Components | JmjC domain-containing histone demethylation protein 1D | ||||||
Keywords | H3K4ME3 BINDING PROTEIN / TRANSFERASE / Jumonji domain lysine demethylase / Metal-binding / Zinc-finger | ||||||
Function / homology | Function and homology information histone H4K20 demethylase activity / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / midbrain development / histone H3K9 demethylase activity / histone demethylase activity / methylated histone binding ...histone H4K20 demethylase activity / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / midbrain development / histone H3K9 demethylase activity / histone demethylase activity / methylated histone binding / transcription coregulator activity / HDMs demethylate histones / Signaling by BRAF and RAF1 fusions / iron ion binding / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Horton, J.R. / Upadhyay, A.K. / Qi, H.H. / Zhang, X. / Shi, Y. / Cheng, X. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Authors: Horton, J.R. / Upadhyay, A.K. / Qi, H.H. / Zhang, X. / Shi, Y. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kva.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kva.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 3kva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/3kva ftp://data.pdbj.org/pub/pdb/validation_reports/kv/3kva | HTTPS FTP |
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-Related structure data
Related structure data | 3kv4C 3kv5C 3kv6SC 3kv9C 3kvbC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46081.043 Da / Num. of mol.: 1 / Fragment: UNP Residues 92-488 Source method: isolated from a genetically manipulated source Details: GST-fusion / Source: (gene. exp.) Homo sapiens (human) / Gene: JHDM1D, KIAA1718 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus / References: UniProt: Q6ZMT4, Transferases | ||||||
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#2: Chemical | #3: Chemical | ChemComp-OXY / | #4: Chemical | ChemComp-AKG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.72 % Description: The Structure Factor File contains Friedel pairs |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 17-20% (v/v) polyethylene glycol 5000 MME, 0.2 M CaCl2, and 0.1 M BisTris pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.27046 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.27046 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→34.4 Å / Num. obs: 26944 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.79→2.89 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1360 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KV6 Resolution: 2.79→34.4 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 555080.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.4081 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.79→34.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.79→2.89 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
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Xplor file |
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