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Yorodumi- PDB-2pwn: Crystal structure of BET3 homolog (13277653) from Mus musculus at... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pwn | |||||||||
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Title | Crystal structure of BET3 homolog (13277653) from Mus musculus at 2.04 A resolution | |||||||||
Components | Trafficking protein particle complex subunit 3 | |||||||||
Keywords | TRANSPORT PROTEIN / 13277653 / Transport protein particle (TRAPP) component / Bet3 / BET3 homolog / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | |||||||||
Function / homology | Function and homology information vesicle coating / vesicle tethering / RAB GEFs exchange GTP for GDP on RABs / COPII-mediated vesicle transport / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / cis-Golgi network membrane / COPII vesicle coating / intra-Golgi vesicle-mediated transport ...vesicle coating / vesicle tethering / RAB GEFs exchange GTP for GDP on RABs / COPII-mediated vesicle transport / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / cis-Golgi network membrane / COPII vesicle coating / intra-Golgi vesicle-mediated transport / endoplasmic reticulum to Golgi vesicle-mediated transport / Golgi membrane / endoplasmic reticulum / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.04 Å | |||||||||
Authors | Joint Center for Structural Genomics (JCSG) | |||||||||
Citation | Journal: To be published Title: Crystal structure of BET3 homolog (13277653) from Mus musculus at 2.04 A resolution Authors: Joint Center for Structural Genomics (JCSG) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pwn.cif.gz | 45.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pwn.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 2pwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pwn_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 2pwn_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 2pwn_validation.xml.gz | 9 KB | Display | |
Data in CIF | 2pwn_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/2pwn ftp://data.pdbj.org/pub/pdb/validation_reports/pw/2pwn | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22160.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: 13277653, Trappc3, Bet3 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: O55013 |
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#2: Chemical | ChemComp-MYR / |
#3: 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: 2.22 Å3/Da / Density % sol: 44.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: NANODROP, 0.4M NH4H2PO3, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99987, 0.97969, 0.97957 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.04→23.156 Å / Num. obs: 12800 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 38.47 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.04→23.156 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.436 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.162 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. MYRISTIC ACID MODELED BASED ON RELATED STRUCTURE (1WC9). 4. CYS 68 IS COVALENTLY ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. MYRISTIC ACID MODELED BASED ON RELATED STRUCTURE (1WC9). 4. CYS 68 IS COVALENTLY BOUND TO MYRISTIC ACID. 5. THERE WAS INSUFFICIENT DENSITY TO MODEL RESIDUES 117-120.
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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: 41.498 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→23.156 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.093 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 35.842 Å / Origin y: 39.124 Å / Origin z: 8.13 Å
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Refinement TLS group | Selection: ALL |