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- PDB-7bjn: Crystal structure of atypical Tm1 (Tm1-I/C), residues 270-334 -

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Basic information

Entry
Database: PDB / ID: 7bjn
TitleCrystal structure of atypical Tm1 (Tm1-I/C), residues 270-334
ComponentsSD21996p
KeywordsTRANSPORT PROTEIN / coiled-coil / mRNA transport / interaction with Khc / Drosophila oocyte
Function / homologyTropomyosin / Tropomyosin / SD21996p
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDimitrova-Paternoga, L. / Jagtap, P.K.A. / Ephrussi, A. / Hennig, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP 1935 Germany
CitationJournal: 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
DepositionJan 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SD21996p
B: SD21996p


Theoretical massNumber of molelcules
Total (without water)15,2992
Polymers15,2992
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-20 kcal/mol
Surface area7970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.880, 127.880, 34.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein SD21996p / Tropomyosin 1 / isoform H


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 / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.67 Å3/Da / Density % sol: 73.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M NH4Ac pH 4.6, 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.365.0660.9841.3333646766640.5591.09798.2
2.36-2.425.3680.7651.9236936886880.7610.848100
2.42-2.495.2980.6332.334546526520.790.704100
2.49-2.575.2030.522.7132836326310.850.57899.8
2.57-2.655.0830.413.430706056040.8840.45899.8
2.65-2.754.9010.3463.8929265985970.9390.38899.8
2.75-2.855.2630.2565.7730425785780.9460.285100
2.85-2.975.4040.2076.8429295425420.9730.229100
2.97-3.15.3630.1589.329715545540.9810.175100
3.1-3.255.3350.12311.2224704644630.990.13799.8
3.25-3.435.190.09814.2225694984950.9930.1199.4
3.43-3.634.8570.07916.1721714474470.9940.089100
3.63-3.885.5310.06820.7724174374370.9960.075100
3.88-4.25.4790.05922.5921373903900.9970.065100
4.2-4.65.2930.05724.3518953583580.9970.064100
4.6-5.144.9440.05423.5416713383380.9970.06100
5.14-5.935.3040.07218.9915172872860.9960.0899.7
5.93-7.275.4110.06122.3113422492480.9970.06899.6
7.27-10.284.9570.03631.559221861860.9980.04100
10.28-63.945.50.03337.355831071060.9990.03799.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
AMPLEphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2695 464 5.01 %
Rwork0.234 8795 -
obs0.2357 9259 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.1 Å2 / Biso mean: 78.4922 Å2 / Biso min: 33.85 Å2
Refinement stepCycle: final / Resolution: 2.3→63.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 0 0 14 789
Biso mean---62.06 -
Num. residues----102
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.630.31351540.26682916307099
2.63-3.310.34081550.272729463101100
3.32-63.940.23521550.21329333088100

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