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- PDB-8sii: Crystal Structure of CBX7 with compound UNC4976 -

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Basic information

Entry
Database: PDB / ID: 8sii
TitleCrystal Structure of CBX7 with compound UNC4976
Components
  • Chromobox protein homolog 7
  • UNC4976
KeywordsTRANSCRIPTION / CBX7 / UNC4976 / SGC / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium
Function / homology
Function and homology information


PRC1 complex / PcG protein complex / chromatin organization / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Chromobox protein homolog 7 / CBX family C-terminal motif / CBX family C-terminal motif / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain ...Chromobox protein homolog 7 / CBX family C-terminal motif / CBX family C-terminal motif / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily
Similarity search - Domain/homology
Chromobox protein homolog 7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsSong, X. / Dong, A. / Huang, R. / 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: Crystal Structure of CBX7 with compound UNC4976
Authors: Song, X. / Dong, A. / Huang, R. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionApr 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 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: Chromobox protein homolog 7
B: Chromobox protein homolog 7
F: UNC4976
G: UNC4976
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,78810
Polymers15,3284
Non-polymers4606
Water2,558142
1
A: Chromobox protein homolog 7
F: UNC4976
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8965
Polymers7,6642
Non-polymers2323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-34 kcal/mol
Surface area4680 Å2
MethodPISA
2
B: Chromobox protein homolog 7
G: UNC4976
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8925
Polymers7,6642
Non-polymers2283
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-34 kcal/mol
Surface area4630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.735, 40.514, 83.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABFG

#1: Protein Chromobox protein homolog 7


Mass: 6816.852 Da / Num. of mol.: 2 / Fragment: chromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX7 / Production host: Escherichia coli (E. coli) / References: UniProt: O95931
#2: Protein/peptide UNC4976


Mass: 847.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 148 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.5 M Ammonium Sulfate, 0.1 M 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: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 26991 / % possible obs: 94.9 % / Redundancy: 6.5 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.029 / Rrim(I) all: 0.075 / Χ2: 1.852 / Net I/σ(I): 10.4 / Num. measured all: 175688
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.37-1.393.20.43111180.6590.8910.2740.5140.9480.4
1.39-1.423.80.35412060.8670.9640.2020.4110.78988
1.42-1.454.30.35313090.860.9620.1910.4050.78892.3
1.45-1.484.90.30813450.920.9790.1530.3460.82697.7
1.48-1.515.90.25614010.9290.9820.1170.2830.87299.6
1.51-1.547.60.2313990.9690.9920.0890.2470.93299.9
1.54-1.5880.19613860.9840.9960.0740.210.96699.9
1.58-1.6280.18314200.980.9950.0690.1961.04199.9
1.62-1.678.10.15413890.9870.9970.0580.1651.17799.8
1.67-1.737.70.13914040.9850.9960.0540.1491.29499.7
1.73-1.797.40.12214030.9880.9970.050.1331.47499.8
1.79-1.866.70.10914280.9880.9970.0470.1191.65999.9
1.86-1.945.20.09811330.9890.9970.0470.1091.93180.1
1.94-2.057.40.08414180.9930.9980.0350.0922.2299.6
2.05-2.1770.0813970.9940.9990.0340.0872.66399.6
2.17-2.346.30.07210660.9950.9990.0320.0792.74274.6
2.34-2.586.80.06614430.9950.9990.0280.0722.7899.2
2.58-2.956.80.06214340.9960.9990.0260.0683.21499.2
2.95-3.7270.05813780.9960.9990.0240.0633.75993.2
3.72-506.70.05415140.9960.9990.0220.0583.48696.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→36.45 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 0.966 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22295 1399 5.2 %RANDOM
Rwork0.19683 ---
obs0.19816 25544 94.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.316 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0 Å20 Å2
2--0.74 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.37→36.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 144 142 1246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131170
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181122
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.661589
X-RAY DIFFRACTIONr_angle_other_deg1.1751.7622610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3975118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.52620.8261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13415202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4991510
X-RAY DIFFRACTIONr_chiral_restr0.0580.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02260
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_it0.9861.506464
X-RAY DIFFRACTIONr_mcbond_other0.9781.503461
X-RAY DIFFRACTIONr_mcangle_it1.6992.251578
X-RAY DIFFRACTIONr_mcangle_other1.6992.251578
X-RAY DIFFRACTIONr_scbond_it1.271.698706
X-RAY DIFFRACTIONr_scbond_other1.231.666691
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9752.422986
X-RAY DIFFRACTIONr_long_range_B_refined3.76617.6271246
X-RAY DIFFRACTIONr_long_range_B_other3.60616.9911215
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.37→1.403 Å
RfactorNum. reflection% reflection
Rfree0.271 90 -
Rwork0.267 1614 -
obs--82.28 %

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