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- PDB-7n27: Crystal Structure of chromodomain of CDYL in complex with inhibit... -

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Basic information

Entry
Database: PDB / ID: 7n27
TitleCrystal Structure of chromodomain of CDYL in complex with inhibitor UNC6261
Components
  • Isoform 2 of Chromodomain Y-like protein
  • inhibitor UNC6261
KeywordsTRANSCRIPTION / Chromodomain Y-like protein / transcription regulation / spermatogenesis / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of peptidyl-lysine crotonylation / (2E)-butenoyl-CoA hydratase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / random inactivation of X chromosome / spermatid development / transcription corepressor activity / chromosome / spermatogenesis / protein-macromolecule adaptor activity / nuclear speck ...negative regulation of peptidyl-lysine crotonylation / (2E)-butenoyl-CoA hydratase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / random inactivation of X chromosome / spermatid development / transcription corepressor activity / chromosome / spermatogenesis / protein-macromolecule adaptor activity / nuclear speck / chromatin binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / Chromo domain, conserved site / Enoyl-CoA hydratase, C-terminal / Chromo domain signature. / 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 ...: / Chromo domain, conserved site / Enoyl-CoA hydratase, C-terminal / Chromo domain signature. / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBeldar, S. / Dong, A. / Loppnau, P. / Min, J. / Arrowsmith, C.H. / Edwards, A.M. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal Structure of chromodomain of CDYL in complex with inhibitor UNC6261
Authors: Beldar, S. / Dong, A. / Loppnau, P. / Min, J. / Arrowsmith, C.H. / Edwards, A.M. / Structural Genomics Consortium (SGC)
History
DepositionMay 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _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: Isoform 2 of Chromodomain Y-like protein
G: inhibitor UNC6261
B: Isoform 2 of Chromodomain Y-like protein
H: inhibitor UNC6261
C: Isoform 2 of Chromodomain Y-like protein
I: inhibitor UNC6261
D: Isoform 2 of Chromodomain Y-like protein
J: inhibitor UNC6261
E: Isoform 2 of Chromodomain Y-like protein
K: inhibitor UNC6261
F: Isoform 2 of Chromodomain Y-like protein
L: inhibitor UNC6261
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,32116
Polymers48,27512
Non-polymers464
Water1,24369
1
A: Isoform 2 of Chromodomain Y-like protein
G: inhibitor UNC6261
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0693
Polymers8,0462
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-2 kcal/mol
Surface area4360 Å2
MethodPISA
2
B: Isoform 2 of Chromodomain Y-like protein
H: inhibitor UNC6261


Theoretical massNumber of molelcules
Total (without water)8,0462
Polymers8,0462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-1 kcal/mol
Surface area4500 Å2
MethodPISA
3
C: Isoform 2 of Chromodomain Y-like protein
I: inhibitor UNC6261


Theoretical massNumber of molelcules
Total (without water)8,0462
Polymers8,0462
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-10 kcal/mol
Surface area4490 Å2
MethodPISA
4
D: Isoform 2 of Chromodomain Y-like protein
J: inhibitor UNC6261
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0694
Polymers8,0462
Non-polymers232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-9 kcal/mol
Surface area4700 Å2
MethodPISA
5
E: Isoform 2 of Chromodomain Y-like protein
K: inhibitor UNC6261


Theoretical massNumber of molelcules
Total (without water)8,0462
Polymers8,0462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-1 kcal/mol
Surface area4290 Å2
MethodPISA
6
F: Isoform 2 of Chromodomain Y-like protein
L: inhibitor UNC6261


Theoretical massNumber of molelcules
Total (without water)8,0463
Polymers8,0462
Non-polymers01
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-1 kcal/mol
Surface area4610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.971, 76.386, 80.628
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
Isoform 2 of Chromodomain Y-like protein / CDY-like / Crotonyl-CoA hydratase


Mass: 7125.817 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDYL, CDYL1 / Plasmid: pGEX-MHL / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9Y232, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Protein/peptide
inhibitor UNC6261


Mass: 919.979 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.01 Å3/Da / Density % sol: 38.76 % / Mosaicity: 0.837 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.5M Na Formate, 0.1M Bis-Tris propane pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 33365 / % possible obs: 99.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.5
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.752 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V41

6v41


Resolution: 1.85→48.64 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.421 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1542 4.6 %RANDOM
Rwork0.225 ---
obs0.227 31770 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å20 Å20 Å2
2---2.27 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 4 69 3264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0143293
X-RAY DIFFRACTIONr_bond_other_d0.0090.0192732
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.7514469
X-RAY DIFFRACTIONr_angle_other_deg2.4271.7526304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9385362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61621.971208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23915473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0141527
X-RAY DIFFRACTIONr_chiral_restr0.0630.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023679
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02749
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 86 -
Rwork0.336 2054 -
obs--87.13 %

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