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- PDB-7slw: Complex structure of CDYL2 with an antagonist -

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Basic information

Entry
Database: PDB / ID: 7slw
TitleComplex structure of CDYL2 with an antagonist
Components(Chromodomain Y-like protein 2) x 2
KeywordsTRANSCRIPTION / chromodomain Y-like protein / transcription regulation / spermatogenesis / Structural Genomics / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBeldar, S. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Complex structure of CDYL2 with an antagonist
Authors: Beldar, S. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionOct 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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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
G: Chromodomain Y-like protein 2
B: Chromodomain Y-like protein 2
H: Chromodomain Y-like protein 2
C: Chromodomain Y-like protein 2
I: Chromodomain Y-like protein 2
D: Chromodomain Y-like protein 2
J: Chromodomain Y-like protein 2
E: Chromodomain Y-like protein 2
K: Chromodomain Y-like protein 2
F: Chromodomain Y-like protein 2
L: Chromodomain Y-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,79816
Polymers49,70612
Non-polymers924
Water1629
1
A: Chromodomain Y-like protein 2
G: Chromodomain Y-like protein 2
B: Chromodomain Y-like protein 2
H: Chromodomain Y-like protein 2
C: Chromodomain Y-like protein 2
I: Chromodomain Y-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9458
Polymers24,8536
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-39 kcal/mol
Surface area9740 Å2
MethodPISA
2
D: Chromodomain Y-like protein 2
J: Chromodomain Y-like protein 2
E: Chromodomain Y-like protein 2
K: Chromodomain Y-like protein 2
F: Chromodomain Y-like protein 2
L: Chromodomain Y-like protein 2


Theoretical massNumber of molelcules
Total (without water)24,8538
Polymers24,8536
Non-polymers02
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-41 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.953, 81.265, 122.741
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Fragment: chromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDYL2 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: Q8N8U2
#2: Protein/peptide
Chromodomain Y-like protein 2


Mass: 833.068 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDYL2 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.28 Å3/Da / Density % sol: 45.94 % / Mosaicity: 0.478 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3350, 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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20142 / % possible obs: 96.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.032 / Rrim(I) all: 0.076 / Χ2: 0.952 / Net I/σ(I): 8.6 / Num. measured all: 112647
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.343.80.5557530.7880.270.620.60674
2.34-2.384.10.4898260.7950.2360.5460.63580.7
2.38-2.434.20.5059280.230.2610.5730.74892.2
2.43-2.484.50.4269770.8910.2060.4760.65395.9
2.48-2.534.90.42610070.8920.2050.4750.64998.8
2.53-2.595.20.37910060.9440.180.420.64499.7
2.59-2.665.90.36610410.9640.1630.4010.66399.7
2.66-2.736.10.35110140.9450.1550.3850.7799.9
2.73-2.816.30.26310290.970.1130.2870.7499.8
2.81-2.96.70.20810130.9820.0860.2250.843100
2.9-36.60.18410320.9850.0770.1990.8999.9
3-3.126.60.14210310.9910.060.1550.957100
3.12-3.266.40.10210310.9950.0440.1111.01899.9
3.26-3.446.20.08910410.9960.0390.0971.15599.8
3.44-3.655.60.0710200.9950.0330.0781.30999.3
3.65-3.935.50.06210410.9960.030.0691.43799.5
3.93-4.335.50.05210430.9950.0260.0581.42999.1
4.33-4.955.70.04510690.9960.0220.051.12599.8
4.95-6.245.80.04510790.9960.0210.0491.194100
6.24-505.30.03611610.9990.0170.041.03299.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hae

4hae


Resolution: 2.3→49.02 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 24.245 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.401 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1061 5.3 %RANDOM
Rwork0.2418 ---
obs0.244 19030 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.27 Å2 / Biso mean: 58.625 Å2 / Biso min: 39.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å2-0 Å2
2---1.98 Å20 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 2.3→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 9 9 3155
Biso mean--61.25 55.05 -
Num. residues----370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133244
X-RAY DIFFRACTIONr_bond_other_d0.0020.0182759
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.7494407
X-RAY DIFFRACTIONr_angle_other_deg1.1281.7326365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1265352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.21222.757185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90715463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9671517
X-RAY DIFFRACTIONr_chiral_restr0.0950.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023614
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02767
LS refinement shellResolution: 2.3→2.358 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.397 51 -
Rwork0.377 1064 -
obs--74.73 %
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)
16.90391.63921.91695.57820.27045.005-0.1633-0.13730.2984-0.17320.03090.35560.09990.05380.13230.0859-0.0016-0.05630.0198-0.03420.19576.30713.73116.264
25.09810.10414.01027.1487-0.65728.80870.2441-0.0117-0.14680.1756-0.3058-0.19140.76590.02990.06170.17640.0292-0.04810.1083-0.02130.158421.62317.25833.7
38.4633-0.8561-0.89767.19960.03974.20490.08240.02980.558-0.7585-0.0814-0.3054-0.52420.1297-0.00090.3073-0.08790.01960.04670.02160.12320.72232.32816.863
46.58870.42182.51461.7574-0.84472.85820.2711-0.421-0.16840.52-0.15590.12190.1679-0.1772-0.11520.2863-0.0866-0.06580.04480.02440.3648-11.115-0.54310.541
56.72921.81681.34116.45150.28292.6917-0.112-0.30190.6007-0.4615-0.1770.1306-0.3651-0.13710.2890.14960.0562-0.07370.0349-0.06390.2385-27.6191.443-6.009
64.4878-1.0828-2.60833.53550.80825.3246-0.1360.09760.0257-0.4450.0148-0.52450.01890.18470.12120.17790.01280.04750.02550.02410.3408-11.761-15.378-7.81
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 58
2X-RAY DIFFRACTION1G1000 - 1005
3X-RAY DIFFRACTION2B3 - 58
4X-RAY DIFFRACTION2H1000 - 1005
5X-RAY DIFFRACTION2A1101
6X-RAY DIFFRACTION3C4 - 58
7X-RAY DIFFRACTION3I1000 - 1005
8X-RAY DIFFRACTION4D2 - 58
9X-RAY DIFFRACTION4J1000 - 1005
10X-RAY DIFFRACTION5E2 - 58
11X-RAY DIFFRACTION5K1000 - 1005
12X-RAY DIFFRACTION6F1 - 58
13X-RAY DIFFRACTION6L1000 - 1005

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