+Open data
-Basic information
Entry | Database: PDB / ID: 6cvz | ||||||
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Title | Crystal structure of the WD40-repeat of RFWD3 | ||||||
Components | E3 ubiquitin-protein ligase RFWD3 | ||||||
Keywords | TRANSFERASE / WD40-repeat / RFWD3 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information programmed DNA elimination by chromosome breakage / regulation of DNA damage checkpoint / response to ionizing radiation / replication fork processing / site of DNA damage / interstrand cross-link repair / MDM2/MDM4 family protein binding / mitotic G1 DNA damage checkpoint signaling / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase ...programmed DNA elimination by chromosome breakage / regulation of DNA damage checkpoint / response to ionizing radiation / replication fork processing / site of DNA damage / interstrand cross-link repair / MDM2/MDM4 family protein binding / mitotic G1 DNA damage checkpoint signaling / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / PML body / ubiquitin protein ligase activity / p53 binding / protein ubiquitination / DNA damage response / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | DONG, A. / LOPPNAU, P. / SEITOVA, A. / HUTCHINSON, A. / TEMPEL, W. / WEI, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. ...DONG, A. / LOPPNAU, P. / SEITOVA, A. / HUTCHINSON, A. / TEMPEL, W. / WEI, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / TONG, Y. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Proteins / Year: 2019 Title: Target highlights in CASP13: Experimental target structures through the eyes of their authors. Authors: Lepore, R. / Kryshtafovych, A. / Alahuhta, M. / Veraszto, H.A. / Bomble, Y.J. / Bufton, J.C. / Bullock, A.N. / Caba, C. / Cao, H. / Davies, O.R. / Desfosses, A. / Dunne, M. / Fidelis, K. / ...Authors: Lepore, R. / Kryshtafovych, A. / Alahuhta, M. / Veraszto, H.A. / Bomble, Y.J. / Bufton, J.C. / Bullock, A.N. / Caba, C. / Cao, H. / Davies, O.R. / Desfosses, A. / Dunne, M. / Fidelis, K. / Goulding, C.W. / Gurusaran, M. / Gutsche, I. / Harding, C.J. / Hartmann, M.D. / Hayes, C.S. / Joachimiak, A. / Leiman, P.G. / Loppnau, P. / Lovering, A.L. / Lunin, V.V. / Michalska, K. / Mir-Sanchis, I. / Mitra, A.K. / Moult, J. / Phillips Jr., G.N. / Pinkas, D.M. / Rice, P.A. / Tong, Y. / Topf, M. / Walton, J.D. / Schwede, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cvz.cif.gz | 210.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cvz.ent.gz | 165.4 KB | Display | PDB format |
PDBx/mmJSON format | 6cvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/6cvz ftp://data.pdbj.org/pub/pdb/validation_reports/cv/6cvz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 38798.969 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RFWD3, RNF201 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 References: UniProt: Q6PCD5, RING-type E3 ubiquitin transferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 47.08 % / Mosaicity: 0.36 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 16% PEG 3500, 0.2 M Magnesium Chloride, 0.1 M Tris pH8.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→30 Å / Num. obs: 96621 / % possible obs: 99.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.049 / Rrim(I) all: 0.099 / Χ2: 1.969 / Net I/σ(I): 7.4 / Num. measured all: 397184 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: unpublished model Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.723 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.125 / 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: 92.78 Å2 / Biso mean: 35.75 Å2 / Biso min: 10.36 Å2
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Refinement step | Cycle: final / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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