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- PDB-5lxn: Coiled-coil protein -

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Basic information

Entry
Database: PDB / ID: 5lxn
TitleCoiled-coil protein
ComponentsTransforming acidic coiled-coil-containing protein 3
KeywordsSTRUCTURAL PROTEIN / Coiled coil protein / tacc3 / fusion protein / cc2 / fgfr fusion / fgfr3 / fgfr / cancer
Function / homology
Function and homology information


microtubule cytoskeleton organization involved in mitosis / metaphase/anaphase transition of mitotic cell cycle / centriolar satellite / 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 / mitotic spindle / spindle pole ...microtubule cytoskeleton organization involved in mitosis / metaphase/anaphase transition of mitotic cell cycle / centriolar satellite / 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 / mitotic spindle / spindle pole / microtubule cytoskeleton organization / cell population proliferation / cell division / intracellular membrane-bounded organelle / 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
TRIETHYLENE GLYCOL / Transforming acidic coiled-coil-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.08 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)76,83117
Polymers75,5878
Non-polymers1,2439
Water8,305461
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)19,3475
Polymers18,8972
Non-polymers4513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-26 kcal/mol
Surface area12600 Å2
MethodPISA
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)19,2395
Polymers18,8972
Non-polymers3423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-49 kcal/mol
Surface area12770 Å2
MethodPISA
3
E: Transforming acidic coiled-coil-containing protein 3
F: 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
Buried area3630 Å2
ΔGint-49 kcal/mol
Surface area12220 Å2
MethodPISA
4
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)19,3475
Polymers18,8972
Non-polymers4513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-18 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.389, 76.780, 86.832
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.989 Å3/Da / Density % sol: 58.9 %
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: 0.97957, 0.97972, 0.96810, 0.99132
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2015 / Details: Mirrors
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979571
20.979721
30.96811
40.991321
ReflectionResolution: 2.08→28.76 Å / Num. obs: 37552 / % possible obs: 82.5 % / Redundancy: 13.8 % / Biso Wilson estimate: 22.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.4
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.7 / CC1/2: 0.793 / % possible all: 33.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSNovember 4, 2014data reduction
Aimless0.3.11data scaling
SHELXCD0.3.i-betaphasing
RefinementMethod to determine structure: MAD / Resolution: 2.08→28.759 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 38.06
RfactorNum. reflection% reflectionSelection details
Rfree0.2854 1909 5.09 %Random selection
Rwork0.2269 ---
obs0.2291 37536 82.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.2 Å2
Refinement stepCycle: LAST / Resolution: 2.08→28.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5137 0 80 461 5678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045363
X-RAY DIFFRACTIONf_angle_d0.7957127
X-RAY DIFFRACTIONf_dihedral_angle_d19.5152242
X-RAY DIFFRACTIONf_chiral_restr0.029804
X-RAY DIFFRACTIONf_plane_restr0.003934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0797-2.13160.382830.29331026X-RAY DIFFRACTION32
2.1316-2.18920.3569810.30071295X-RAY DIFFRACTION40
2.1892-2.25360.3524790.2991548X-RAY DIFFRACTION49
2.2536-2.32630.3391020.29121869X-RAY DIFFRACTION57
2.3263-2.40930.36021200.27632318X-RAY DIFFRACTION72
2.4093-2.50570.37751410.27652956X-RAY DIFFRACTION92
2.5057-2.61960.28681420.26763054X-RAY DIFFRACTION94
2.6196-2.75750.3181530.26083067X-RAY DIFFRACTION94
2.7575-2.92990.33061540.25453038X-RAY DIFFRACTION94
2.9299-3.15560.3461710.24623071X-RAY DIFFRACTION94
3.1556-3.47220.32051770.23033045X-RAY DIFFRACTION94
3.4722-3.97230.23291630.19213073X-RAY DIFFRACTION95
3.9723-4.99610.23881750.17973087X-RAY DIFFRACTION94
4.9961-22.88380.23651560.20253171X-RAY DIFFRACTION95

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