+Open data
-Basic information
Entry | Database: PDB / ID: 4a5z | ||||||
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Title | Structures of MITD1 | ||||||
Components | MIT DOMAIN-CONTAINING PROTEIN 1 | ||||||
Keywords | PROTEIN TRANSPORT / ESCRT / CYTOKINESIS / MIDBODY | ||||||
Function / homology | Function and homology information midbody abscission / mitotic cytokinesis / phosphatidylinositol binding / negative regulation of protein binding / late endosome membrane / midbody / protein domain specific binding / intracellular membrane-bounded organelle / extracellular exosome / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Hadders, M.A. / Agromayor, M. / Caballe, A. / Obita, T. / Perisic, O. / Williams, R.L. / Martin-Serrano, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Escrt-III Binding Protein Mitd1 is Involved in Cytokinesis and Has an Unanticipated Pld Fold that Binds Membranes. Authors: Hadders, M.A. / Agromayor, M. / Obita, T. / Perisic, O. / Caballe, A. / Kloc, M. / Lamers, M.H. / Williams, R.L. / Martin-Serrano, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a5z.cif.gz | 266.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a5z.ent.gz | 226.7 KB | Display | PDB format |
PDBx/mmJSON format | 4a5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/4a5z ftp://data.pdbj.org/pub/pdb/validation_reports/a5/4a5z | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 19724.662 Da / Num. of mol.: 4 / Fragment: RESIDUES 90-243 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): C41 / References: UniProt: Q8WV92 #2: Chemical | ChemComp-DMS / | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LYS 90 TO ASP ENGINEERED RESIDUE IN CHAIN A, LYS 243 TO ASP ...ENGINEERED | |
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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: 2.5 Å3/Da / Density % sol: 50.9 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 200 MM NACL, 100 MM BISTRIS PH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98050, 0.98070, 0.95000 | ||||||||||||
Detector | Type: ADSC CCD / Detector: CCD | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→73.2 Å / Num. obs: 34453 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 12.1 | ||||||||||||
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.8 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.3→73.2 Å / Cor.coef. Fo:Fc: 0.9207 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / σ(F): 0 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=DMS CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5468. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=4. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=DMS CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5468. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=4. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
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Displacement parameters | Biso mean: 21.67 Å2
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Refine analyze | Luzzati coordinate error obs: 0.258 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→73.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.37 Å / Total num. of bins used: 17
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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