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- PDB-8oyk: Coiled-Coil Domain of Human STIL, L736E Mutant -

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Basic information

Entry
Database: PDB / ID: 8oyk
TitleCoiled-Coil Domain of Human STIL, L736E Mutant
ComponentsIsoform 2 of SCL-interrupting locus protein
KeywordsSTRUCTURAL PROTEIN / STIL / coiled coil / dimer / antiparallel
Function / homology
Function and homology information


floor plate development / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / embryonic axis specification / positive regulation of spindle assembly / notochord development / determination of left/right symmetry / protein localization to centrosome / neural tube development ...floor plate development / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / embryonic axis specification / positive regulation of spindle assembly / notochord development / determination of left/right symmetry / protein localization to centrosome / neural tube development / smoothened signaling pathway / heart looping / centrosome duplication / positive regulation of G1/S transition of mitotic cell cycle / regulation of mitotic spindle organization / forebrain development / centriole / mitotic spindle organization / neural tube closure / multicellular organism growth / cell cortex / in utero embryonic development / centrosome / negative regulation of apoptotic process / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
SCL-interrupting locus protein / SCL-interrupting locus protein N-terminus
Similarity search - Domain/homology
SCL-interrupting locus protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.9 Å
AuthorsMartin, F.J.O. / Shamir, M. / Woolfson, D.N. / Friedler, A.
Funding supportEuropean Union, United Kingdom, Israel, 4items
OrganizationGrant numberCountry
European Research Council (ERC)340764European Union
Engineering and Physical Sciences Research CouncilEP/G036764 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB R00661X 1 United Kingdom
Israel Science Foundation939/14 Israel
CitationJournal: Int J Mol Sci / Year: 2023
Title: Molecular Mechanism of STIL Coiled-Coil Domain Oligomerization.
Authors: Shamir, M. / Martin, F.J.O. / Woolfson, D.N. / Friedler, A.
History
DepositionMay 5, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionOct 18, 2023ID: 7QXG
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of SCL-interrupting locus protein
B: Isoform 2 of SCL-interrupting locus protein
C: Isoform 2 of SCL-interrupting locus protein
D: Isoform 2 of SCL-interrupting locus protein
E: Isoform 2 of SCL-interrupting locus protein
F: Isoform 2 of SCL-interrupting locus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0417
Polymers23,0066
Non-polymers351
Water1,892105
1
A: Isoform 2 of SCL-interrupting locus protein
B: Isoform 2 of SCL-interrupting locus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7043
Polymers7,6692
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-18 kcal/mol
Surface area5480 Å2
2
C: Isoform 2 of SCL-interrupting locus protein
E: Isoform 2 of SCL-interrupting locus protein


Theoretical massNumber of molelcules
Total (without water)7,6692
Polymers7,6692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-13 kcal/mol
Surface area4790 Å2
3
D: Isoform 2 of SCL-interrupting locus protein
F: Isoform 2 of SCL-interrupting locus protein


Theoretical massNumber of molelcules
Total (without water)7,6692
Polymers7,6692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-15 kcal/mol
Surface area5020 Å2
Unit cell
Length a, b, c (Å)43.539, 31.269, 64.473
Angle α, β, γ (deg.)90.00, 98.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Isoform 2 of SCL-interrupting locus protein / TAL-1-interrupting locus protein


Mass: 3834.298 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15468
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.89 Å3/Da / Density % sol: 34.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 0.9 mM peptide, 50 mM Tris, and 10 % v/v MPD, at pH 8.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→63.83 Å / Num. obs: 13477 / % possible obs: 97.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.038 / Rrim(I) all: 0.054 / Net I/σ(I): 15.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 6 / Num. unique obs: 846 / CC1/2: 0.957 / Rpim(I) all: 0.119 / Rrim(I) all: 0.168 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
autoPROC2.2.19data reduction
Aimless0.7.7data scaling
Arcimboldo1.0.21phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.9→63.83 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.311 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22492 680 5 %RANDOM
Rwork0.18048 ---
obs0.18274 12795 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.465 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0.29 Å2
2--0.23 Å20 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.9→63.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 1 105 1655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121609
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161597
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.6542173
X-RAY DIFFRACTIONr_angle_other_deg0.4631.5673633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6035190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.166526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17410315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02432
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7720.955743
X-RAY DIFFRACTIONr_mcbond_other2.6720.955743
X-RAY DIFFRACTIONr_mcangle_it3.2091.679923
X-RAY DIFFRACTIONr_mcangle_other3.2351.683924
X-RAY DIFFRACTIONr_scbond_it6.231.538866
X-RAY DIFFRACTIONr_scbond_other6.2261.539867
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9312.5521245
X-RAY DIFFRACTIONr_long_range_B_refined8.62215.121890
X-RAY DIFFRACTIONr_long_range_B_other8.58214.671870
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 58 -
Rwork0.203 912 -
obs--96.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.34630.25412.07160.9271.36577.396-0.00320.0339-0.034-0.0210.0135-0.018-0.03930.0927-0.01030.02-0.00910.00850.01560.01740.049814.56145.779215.9899
27.47613.14239.20571.87154.780513.2305-0.1567-0.10090.29-0.02210.01070.0949-0.1452-0.06890.1460.00830.00850.00250.00940.00760.083712.754713.702516.513
31.6365-0.13352.96180.664-0.83069.31420.01960.0176-0.06380.00220.03120.0310.06840.0016-0.05080.0320.00740.01680.0099-0.01230.056731.21143.503435.6212
411.6851-0.829511.34253.2681-2.180812.77190.03260.0010.07510.06-0.09740.0143-0.19-0.05440.06480.04020.00930.00950.0147-0.00730.0127-2.49240.05176.6229
54.5619-2.94166.32413.0377-4.473310.505-0.05010.07860.0561-0.05090.0126-0.12430.04460.030.03740.0169-0.01350.01310.0113-0.0110.031734.971510.765528.1585
610.03813.159311.73942.47213.079316.47590.1697-0.42950.02570.1019-0.09030.17560.0891-0.3122-0.07930.05920.02610.03780.1086-0.02580.097-11.8396-0.97628.6591
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION2B1 - 32
3X-RAY DIFFRACTION3C1 - 31
4X-RAY DIFFRACTION4D1 - 29
5X-RAY DIFFRACTION5E1 - 30
6X-RAY DIFFRACTION6F1 - 32

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