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- PDB-8oyl: Coiled-Coil Domain of Human STIL, Q729L Mutant -

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Basic information

Entry
Database: PDB / ID: 8oyl
TitleCoiled-Coil Domain of Human STIL, Q729L Mutant
ComponentsSCL-interrupting locus protein
KeywordsSTRUCTURAL PROTEIN / STIL / coiled coil / tetramer / antiparallel
Function / homology
Function and homology information


floor plate development / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / microtubule organizing center organization / embryonic axis specification / notochord development / positive regulation of spindle assembly / determination of left/right symmetry / protein localization to centrosome ...floor plate development / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / microtubule organizing center organization / embryonic axis specification / notochord development / positive regulation of spindle assembly / determination of left/right symmetry / protein localization to centrosome / neural tube development / smoothened signaling pathway / heart looping / microtubule organizing center / centrosome duplication / positive regulation of G1/S transition of mitotic cell cycle / forebrain development / centriole / regulation of mitotic spindle organization / 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 / cytosol / cytoplasm
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: 1.92 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: 7QXH
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: SCL-interrupting locus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1587
Polymers3,8031
Non-polymers3546
Water21612
1
A: SCL-interrupting locus protein
hetero molecules

A: SCL-interrupting locus protein
hetero molecules

A: SCL-interrupting locus protein
hetero molecules

A: SCL-interrupting locus protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,63028
Polymers15,2134
Non-polymers1,41724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6550 Å2
ΔGint-159 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.974, 34.942, 72.321
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-101-

NA

21A-102-

CD

31A-210-

HOH

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Components

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


Mass: 3803.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15468
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cd
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 1.5 mM peptide, 50 mM Cadmium chloride hemi(pentahydrate), 50 mM Sodium acetate, and 15 % v/v PEG 400, at pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.92→31.46 Å / Num. obs: 2609 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.08 / Rrim(I) all: 0.153 / Net I/σ(I): 7.1
Reflection shellResolution: 1.92→2 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 280 / CC1/2: 0.89 / Rpim(I) all: 0.152 / Rrim(I) all: 0.38 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
DIALSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.92→31.46 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.136 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18954 270 10.4 %RANDOM
Rwork0.14916 ---
obs0.15335 2338 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.162 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0 Å20 Å2
2--1.49 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: 1 / Resolution: 1.92→31.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms268 0 6 12 286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.012268
X-RAY DIFFRACTIONr_bond_other_d0.0010.016273
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.64360
X-RAY DIFFRACTIONr_angle_other_deg0.4191.559623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.071531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.50954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.971049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.050.243
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02315
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0265
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_it1.0251.647127
X-RAY DIFFRACTIONr_mcbond_other1.0221.645127
X-RAY DIFFRACTIONr_mcangle_it1.5672.938157
X-RAY DIFFRACTIONr_mcangle_other1.5762.948158
X-RAY DIFFRACTIONr_scbond_it1.1972.065141
X-RAY DIFFRACTIONr_scbond_other1.1932.071142
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.773.636204
X-RAY DIFFRACTIONr_long_range_B_refined3.07224.151027
X-RAY DIFFRACTIONr_long_range_B_other2.97623.581021
X-RAY DIFFRACTIONr_rigid_bond_restr3.3253541
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 20 -
Rwork0.16 161 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 3.9407 Å / Origin y: 11.519 Å / Origin z: 34.9292 Å
111213212223313233
T0.0286 Å2-0.0001 Å20.0036 Å2-0.0145 Å20.0059 Å2--0.0214 Å2
L0.1765 °20.1972 °2-1.1283 °2-0.4044 °2-1.75 °2--9.2713 °2
S-0.029 Å °-0.0036 Å °-0.0193 Å °0.0287 Å °-0.0257 Å °-0.0259 Å °-0.0225 Å °-0.0073 Å °0.0547 Å °

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