+Open data
-Basic information
Entry | Database: PDB / ID: 2z6p | ||||||
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Title | Crystal Structure of the Ufc1, Ufm1 conjugating enzyme 1 | ||||||
Components | Ufm1-conjugating enzyme 1 | ||||||
Keywords | LIGASE / UFC1 / UFM1 / UBIQUITIN / UBL / Polymorphism / Ubl conjugation pathway | ||||||
Function / homology | Function and homology information UFM1 conjugating enzyme activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / reticulophagy / response to endoplasmic reticulum stress / brain development / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Mizushima , T. / Tatsumi, K. / Ozaki, Y. / Kawakami, T. / Suzuki, A. / Ogasahara, K. / Komatsu, M. / Kominami, E. / Tanaka, K. / Yamane, T. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2007 Title: Crystal structure of Ufc1, the Ufm1-conjugating enzyme Authors: Mizushima, T. / Tatsumi, K. / Ozaki, Y. / Kawakami, T. / Suzuki, A. / Ogasahara, K. / Komatsu, M. / Kominami, E. / Tanaka, K. / Yamane, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z6p.cif.gz | 44.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z6p.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 2z6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z6p ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z6p | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20038.537 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1 / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: Q9Y3C8, ubiquitin-protein ligase |
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#2: 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: 1.96 Å3/Da / Density % sol: 37.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.5M ammonium sulfate, 0.1M MES pH 7.0, 10%(w/v) dioxan, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jul 23, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44.5 Å / Num. obs: 15648 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.332 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→44.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.444 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.862 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→44.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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