+Open data
-Basic information
Entry | Database: PDB / ID: 7bjn | ||||||
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Title | Crystal structure of atypical Tm1 (Tm1-I/C), residues 270-334 | ||||||
Components | SD21996p | ||||||
Keywords | TRANSPORT PROTEIN / coiled-coil / mRNA transport / interaction with Khc / Drosophila oocyte | ||||||
Function / homology | Tropomyosin / Tropomyosin / SD21996p Function and homology information | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Dimitrova-Paternoga, L. / Jagtap, P.K.A. / Ephrussi, A. / Hennig, J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Genes Dev. / Year: 2021 Title: Molecular basis of mRNA transport by a kinesin-1-atypical tropomyosin complex. Authors: Dimitrova-Paternoga, L. / Jagtap, P.K.A. / Cyrklaff, A. / Lapouge, K. / Sehr, P. / Perez, K. / Heber, S. / Low, C. / Hennig, J. / Ephrussi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bjn.cif.gz | 33.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bjn.ent.gz | 21.3 KB | Display | PDB format |
PDBx/mmJSON format | 7bjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bjn_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 7bjn_full_validation.pdf.gz | 434.3 KB | Display | |
Data in XML | 7bjn_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 7bjn_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/7bjn ftp://data.pdbj.org/pub/pdb/validation_reports/bj/7bjn | HTTPS FTP |
-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: 7649.507 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: Tm1, 10, 1305, 2299, BcDNA:GH09289, BcDNA:LD37158, BcDNA:SD21996, chr3R:11122272..11122408, cTM, cTm, cTmII, Dm Tm1, Dm TmH33, Dm TmH34, Dmel\CG4898, DmTm1, l(3)02299, l(3)S130510, l(3)s2958, ...Gene: Tm1, 10, 1305, 2299, BcDNA:GH09289, BcDNA:LD37158, BcDNA:SD21996, chr3R:11122272..11122408, cTM, cTm, cTmII, Dm Tm1, Dm TmH33, Dm TmH34, Dmel\CG4898, DmTm1, l(3)02299, l(3)S130510, l(3)s2958, mTmII, PmI, region 3, TM, Tm, TM1, tm1, TmH, TmH-33, TmH-34, TmH33, TmH34, TMII, TmII, tmII, Tmr33, Tmr34, TnH, TnH-33, TnH-34, tropomyosin, CG4898, Dmel_CG4898 Production host: Escherichia coli (E. coli) / References: UniProt: Q8IG84 #2: 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: 4.67 Å3/Da / Density % sol: 73.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M NH4Ac pH 4.6, 15% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 31, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→63.94 Å / Num. obs: 9264 / % possible obs: 99.8 % / Redundancy: 5.227 % / Biso Wilson estimate: 50.978 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.103 / Χ2: 1.022 / Net I/σ(I): 10.45 / Num. measured all: 48426 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: poly Ala helix Resolution: 2.3→63.94 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 33.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.1 Å2 / Biso mean: 78.4922 Å2 / Biso min: 33.85 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→63.94 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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