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- PDB-5lxo: Coiled-coil protein -

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Basic information

Entry
Database: PDB / ID: 5lxo
TitleCoiled-coil protein
ComponentsTransforming acidic coiled-coil-containing protein 3
KeywordsSTRUCTURAL PROTEIN / TACC3 / coiled-coil / helix / fgfr fusion / fgfr / growth factors / cancer / fusion / parallel helix
Function / homology
Function and homology information


microtubule cytoskeleton organization involved in mitosis / metaphase/anaphase transition of mitotic cell cycle / nuclear migration / regulation of mitotic spindle organization / mitotic spindle organization / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / cerebral cortex development / microtubule cytoskeleton organization / centriolar satellite ...microtubule cytoskeleton organization involved in mitosis / metaphase/anaphase transition of mitotic cell cycle / nuclear migration / regulation of mitotic spindle organization / mitotic spindle organization / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / cerebral cortex development / microtubule cytoskeleton organization / centriolar satellite / spindle pole / mitotic spindle / ciliary basal body / cell division / intracellular membrane-bounded organelle / Golgi apparatus / cytoplasm / cytosol
Similarity search - Function
Transforming acidic coiled-coil-containing protein, C-terminal / TACC family / Transforming acidic coiled-coil-containing protein (TACC), C-terminal
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / Transforming acidic coiled-coil-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.179 Å
AuthorsThiyagarajan, N. / Bunney, T.D. / Katan, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKA16567 United Kingdom
CitationJournal: To Be Published
Title: Coiled-coil protein
Authors: Thiyagarajan, N. / Bunney, T.D. / Katan, M.
History
DepositionSep 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming acidic coiled-coil-containing protein 3
B: Transforming acidic coiled-coil-containing protein 3
C: Transforming acidic coiled-coil-containing protein 3
D: Transforming acidic coiled-coil-containing protein 3
E: Transforming acidic coiled-coil-containing protein 3
F: Transforming acidic coiled-coil-containing protein 3
G: Transforming acidic coiled-coil-containing protein 3
H: Transforming acidic coiled-coil-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,07813
Polymers75,5878
Non-polymers4915
Water6,972387
1
A: Transforming acidic coiled-coil-containing protein 3
B: Transforming acidic coiled-coil-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2025
Polymers18,8972
Non-polymers3053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Transforming acidic coiled-coil-containing protein 3
D: Transforming acidic coiled-coil-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9323
Polymers18,8972
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Transforming acidic coiled-coil-containing protein 3
F: Transforming acidic coiled-coil-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0473
Polymers18,8972
Non-polymers1501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Transforming acidic coiled-coil-containing protein 3
H: Transforming acidic coiled-coil-containing protein 3


Theoretical massNumber of molelcules
Total (without water)18,8972
Polymers18,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.250, 76.460, 86.891
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Transforming acidic coiled-coil-containing protein 3 / ERIC-1


Mass: 9448.420 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Coiled-coil 2 domain / Source: (gene. exp.) Homo sapiens (human) / Gene: TACC3, ERIC1 / Plasmid: pJ821 / Details (production host): Rhamnose induced / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9Y6A5

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Non-polymers , 5 types, 392 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 35 % PEG 400, 0.05 M Sodium sulphate, 0.05 M Lithium sulphate, 0.05 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9681 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2015 / Details: Mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9681 Å / Relative weight: 1
ReflectionResolution: 2.179→28.964 Å / Num. obs: 37534 / % possible obs: 95.5 % / Redundancy: 13.1 % / Biso Wilson estimate: 19.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Net I/σ(I): 21
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.838 / % possible all: 67.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSNov 3, 2014data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LXN

5lxn


Resolution: 2.179→28.964 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.38
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 1844 4.91 %Random selection
Rwork0.2333 ---
obs0.2352 37524 95.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.4 Å2
Refinement stepCycle: LAST / Resolution: 2.179→28.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5094 0 30 387 5511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085266
X-RAY DIFFRACTIONf_angle_d1.0667017
X-RAY DIFFRACTIONf_dihedral_angle_d19.372197
X-RAY DIFFRACTIONf_chiral_restr0.037796
X-RAY DIFFRACTIONf_plane_restr0.005926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1804-2.23930.39251190.33651944X-RAY DIFFRACTION66
2.2393-2.3050.39041130.31952366X-RAY DIFFRACTION78
2.305-2.37930.36541200.29772656X-RAY DIFFRACTION89
2.3793-2.46410.39981270.29962855X-RAY DIFFRACTION95
2.4641-2.56250.37561400.28912824X-RAY DIFFRACTION95
2.5625-2.67870.35731310.27992867X-RAY DIFFRACTION96
2.6787-2.81950.31781360.27152894X-RAY DIFFRACTION96
2.8195-2.99540.36111460.26592866X-RAY DIFFRACTION95
2.9954-3.22540.27691510.24032845X-RAY DIFFRACTION95
3.2254-3.54770.27451230.22662877X-RAY DIFFRACTION96
3.5477-4.05590.23661510.18492878X-RAY DIFFRACTION95
4.0559-5.09060.23381610.17672884X-RAY DIFFRACTION95
5.0906-17.94480.25251560.21782929X-RAY DIFFRACTION95

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