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Yorodumi- PDB-6ydv: Crystal Structure of the Jmjc Domain of Human JMJD1B in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ydv | ||||||
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Title | Crystal Structure of the Jmjc Domain of Human JMJD1B in complex with FM001511a from the DSPL fragment library | ||||||
Components | JMJD1B protein | ||||||
Keywords | OXIDOREDUCTASE / Fragment / Complex / KDM3B / Xchem / Structural Genomics | ||||||
Function / homology | JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / : / Chem-ONQ / JMJD1B protein Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Snee, M. / Nowak, R. / Johansson, C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Oppermann, U. | ||||||
Citation | Journal: To Be Published Title: Crystal Structure of the Jmjc Domain of Human JMJD1B in complex with FM001511a from the DSPL fragment library Authors: Snee, M. / Nowak, R. / Johansson, C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ydv.cif.gz | 518.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ydv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ydv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ydv_validation.pdf.gz | 692.2 KB | Display | wwPDB validaton report |
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Full document | 6ydv_full_validation.pdf.gz | 694.9 KB | Display | |
Data in XML | 6ydv_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 6ydv_validation.cif.gz | 48.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/6ydv ftp://data.pdbj.org/pub/pdb/validation_reports/yd/6ydv | HTTPS FTP |
-Related structure data
Related structure data | 6rbjS 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: 43075.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD1B / Production host: Escherichia coli (E. coli) / References: UniProt: A4FUT8 #2: Chemical | ChemComp-ONQ / ~{ | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M bis-tris pH 5.5, 24% PEG3350, 0.4M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9282 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→54.934 Å / Num. obs: 56778 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.041 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.069 / Rrim(I) all: 0.13 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.07→9.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.961 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4190 / CC1/2: 0.556 / Rpim(I) all: 0.713 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RBJ Resolution: 2.07→54.934 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.146 / SU B: 13.587 / SU ML: 0.149 / Average fsc free: 0.8542 / Average fsc work: 0.8698 / Cross valid method: FREE R-VALUE / ESU R Free: 0.152 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→54.934 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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