+Open data
-Basic information
Entry | Database: PDB / ID: 4ld6 | ||||||
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Title | PWWP domain of human PWWP Domain-Containing Protein 2B | ||||||
Components | PWWP domain-containing protein 2B | ||||||
Keywords | UNKNOWN FUNCTION / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Dong, A. / Dombrovski, L. / Tempel, W. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of PWWP domain of human PWWP Domain-Containing Protein 2B Authors: Dombrovski, L. / Dong, A. / Tempel, W. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ld6.cif.gz | 41.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ld6.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ld6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/4ld6 ftp://data.pdbj.org/pub/pdb/validation_reports/ld/4ld6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13264.072 Da / Num. of mol.: 1 / Fragment: PWWP domain (UNP residues 475-590) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PWWP2B, PWWP2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)V2RpRARE / References: UniProt: Q6NUJ5 | ||
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#2: Chemical | ChemComp-GOL / | ||
#3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG3350, 0.2 M ammonium acetate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.7→50 Å / Num. all: 11827 / Num. obs: 11827 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 56.4 | ||||||||||||||||||
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.7 / Num. unique all: 497 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→28.29 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.841 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.01 Å2 / Biso mean: 17.754 Å2 / Biso min: 8.63 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→28.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.743 Å / Total num. of bins used: 20
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