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- PDB-8sp6: COMPLEX STRUCTURE OF CDYL2 WITH AN ANTAGONIST -

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Basic information

Entry
Database: PDB / ID: 8sp6
TitleCOMPLEX STRUCTURE OF CDYL2 WITH AN ANTAGONIST
Components
  • (5R0)FAL(MLZ)(5R5)
  • Chromodomain Y-like protein 2
KeywordsTRANSCRIPTION / CDYL2 / Antagonist / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


methylated histone binding / transcription corepressor activity / nucleus
Similarity search - Function
Chromo domain, conserved site / Chromo domain signature. / Enoyl-CoA hydratase, C-terminal / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Chromo/chromo shadow domain / Chromatin organization modifier domain ...Chromo domain, conserved site / Chromo domain signature. / Enoyl-CoA hydratase, C-terminal / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
: / Chromodomain Y-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSong, X. / Beldar, S. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: To be published
Title: COMPLEX STRUCTURE OF CDYL2 WITH AN ANTAGONIST
Authors: Song, X. / Beldar, S. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionMay 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromodomain Y-like protein 2
B: Chromodomain Y-like protein 2
C: Chromodomain Y-like protein 2
D: Chromodomain Y-like protein 2
E: Chromodomain Y-like protein 2
F: Chromodomain Y-like protein 2
G: (5R0)FAL(MLZ)(5R5)
H: (5R0)FAL(MLZ)(5R5)
I: (5R0)FAL(MLZ)(5R5)
J: (5R0)FAL(MLZ)(5R5)
K: (5R0)FAL(MLZ)(5R5)
L: (5R0)FAL(MLZ)(5R5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,12519
Polymers49,22612
Non-polymers8997
Water7,476415
1
A: Chromodomain Y-like protein 2
G: (5R0)FAL(MLZ)(5R5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3003
Polymers8,2042
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-9 kcal/mol
Surface area4580 Å2
MethodPISA
2
B: Chromodomain Y-like protein 2
H: (5R0)FAL(MLZ)(5R5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3003
Polymers8,2042
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-8 kcal/mol
Surface area4230 Å2
MethodPISA
3
C: Chromodomain Y-like protein 2
I: (5R0)FAL(MLZ)(5R5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3003
Polymers8,2042
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area4420 Å2
MethodPISA
4
D: Chromodomain Y-like protein 2
J: (5R0)FAL(MLZ)(5R5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6234
Polymers8,2042
Non-polymers4192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-8 kcal/mol
Surface area4580 Å2
MethodPISA
5
E: Chromodomain Y-like protein 2
K: (5R0)FAL(MLZ)(5R5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3003
Polymers8,2042
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-9 kcal/mol
Surface area4360 Å2
MethodPISA
6
F: Chromodomain Y-like protein 2
L: (5R0)FAL(MLZ)(5R5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3003
Polymers8,2042
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-9 kcal/mol
Surface area4190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.905, 88.576, 113.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Chromodomain Y-like protein 2 / CDY-like 2


Mass: 7451.329 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDYL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N8U2
#2: Protein/peptide
(5R0)FAL(MLZ)(5R5)


Mass: 752.940 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 322.358 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical
ChemComp-I9A / (1s,4s)-bicyclo[2.2.1]heptane


Mass: 96.170 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H12 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25.0% PEG3350, 0.2M NH4OAc, 0.1M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 80579 / % possible obs: 97.6 % / Redundancy: 9 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.021 / Rrim(I) all: 0.065 / Χ2: 0.779 / Net I/σ(I): 8.2 / Num. measured all: 728017
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.45-1.486.70.78737430.760.9290.3230.8540.53292.1
1.48-1.57.90.68838780.870.9650.2580.7360.54795.4
1.5-1.538.40.63839560.8880.970.230.6790.5596.2
1.53-1.568.90.54839410.9270.9810.1910.5810.54197.9
1.56-1.69.10.48839720.940.9850.1670.5170.5697.4
1.6-1.639.20.4439910.9520.9880.1490.4650.56797.2
1.63-1.679.20.37840090.9670.9920.1280.40.56198.6
1.67-1.729.20.31739890.9770.9940.1080.3360.59397.6
1.72-1.778.80.24139860.9830.9960.0840.2560.61396.9
1.77-1.8390.1938220.9880.9970.0640.2010.64694.3
1.83-1.899.80.16340680.9940.9980.0530.1710.67498.8
1.89-1.979.80.12840420.9950.9990.0420.1340.70898.6
1.97-2.069.70.140570.9970.9990.0330.1050.77198.6
2.06-2.179.50.07840860.9980.9990.0260.0830.8298.9
2.17-2.39.30.06940700.9980.9990.0230.0730.88398.7
2.3-2.488.70.05941110.99810.0210.0630.9499.4
2.48-2.739.30.05240510.99910.0170.0551.02597.2
2.73-3.129.80.04341760.99910.0140.0461.15599.7
3.12-3.949.40.03542250.99910.0120.0371.3999.9
3.94-508.70.03444060.99810.0120.0361.21399

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HAE

4hae


Resolution: 1.45→47.75 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.387 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23637 4152 5.2 %RANDOM
Rwork0.2144 ---
obs0.21558 76362 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.483 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.45→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 367 415 3632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133418
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183003
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.6394636
X-RAY DIFFRACTIONr_angle_other_deg1.2541.7946956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9795346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.12522.741197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74715513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2611519
X-RAY DIFFRACTIONr_chiral_restr0.0640.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024207
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02798
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_it1.4671.9821393
X-RAY DIFFRACTIONr_mcbond_other1.4611.9791389
X-RAY DIFFRACTIONr_mcangle_it2.3782.9541731
X-RAY DIFFRACTIONr_mcangle_other2.3782.9541731
X-RAY DIFFRACTIONr_scbond_it1.6072.0252025
X-RAY DIFFRACTIONr_scbond_other1.6062.0262026
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5792.9832905
X-RAY DIFFRACTIONr_long_range_B_refined4.62322.5673724
X-RAY DIFFRACTIONr_long_range_B_other4.48722.093640
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.451→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 255 -
Rwork0.308 5264 -
obs--91.33 %

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