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- PDB-4mn3: Chromodomain antagonists that target the polycomb-group methyllys... -

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Basic information

Entry
Database: PDB / ID: 4mn3
TitleChromodomain antagonists that target the polycomb-group methyllysine reader protein Chromobox homolog 7 (CBX7)
Components
  • Chromobox protein homolog 7
  • peptide
KeywordsTRANSCRIPTION REGULATOR / chromobox domain 7
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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 ...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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chromobox protein homolog 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic peptide (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.542 Å
AuthorsChakravarthi, S. / Daze, K. / Douglas, S. / Quon, T. / Dev, A. / Peng, F. / Heller, M. / Boulanger, M.J. / Wulff, J. / Hof, F.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Chromodomain Antagonists That Target the Polycomb-Group Methyllysine Reader Protein Chromobox Homolog 7 (CBX7).
Authors: Simhadri, C. / Daze, K.D. / Douglas, S.F. / Quon, T.T. / Dev, A. / Gignac, M.C. / Peng, F. / Heller, M. / Boulanger, M.J. / Wulff, J.E. / Hof, F.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Structure summary

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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: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0367
Polymers7,4992
Non-polymers5375
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-11 kcal/mol
Surface area4600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.290, 31.860, 38.390
Angle α, β, γ (deg.)90.00, 119.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-104-

MG

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Chromobox protein homolog 7


Mass: 6816.852 Da / Num. of mol.: 1 / Fragment: protein
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 peptide


Mass: 681.824 Da / Num. of mol.: 1 / Fragment: peptide / Source method: obtained synthetically / Source: (synth.) Synthetic peptide (others)

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Non-polymers , 4 types, 45 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL, PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40% ethylene glycol, 0.1M HEPES pH 7.5, 5% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.54→29.5 Å / Num. all: 9095 / Num. obs: 8874 / % possible obs: 90.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 1.54→1.58 Å / % possible all: 86.08

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.542→29.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.6 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21265 431 4.7 %RANDOM
Rwork0.17221 ---
obs0.17416 8664 90.73 %-
all-9095 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.812 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.542→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms531 0 26 40 597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02565
X-RAY DIFFRACTIONr_bond_other_d0.0020.02562
X-RAY DIFFRACTIONr_angle_refined_deg2.1391.999747
X-RAY DIFFRACTIONr_angle_other_deg1.01831302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.046559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.06823.07726
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.22515100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.894154
X-RAY DIFFRACTIONr_chiral_restr0.1630.271
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021572
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02122
X-RAY DIFFRACTIONr_mcbond_it2.2491.897243
X-RAY DIFFRACTIONr_mcbond_other2.1781.893242
X-RAY DIFFRACTIONr_mcangle_it3.3542.851299
X-RAY DIFFRACTIONr_mcangle_other3.3572.851300
X-RAY DIFFRACTIONr_scbond_it3.552.343322
X-RAY DIFFRACTIONr_scbond_other3.5312.342322
X-RAY DIFFRACTIONr_scangle_other5.0173.282449
X-RAY DIFFRACTIONr_long_range_B_refined6.79116.246642
X-RAY DIFFRACTIONr_long_range_B_other6.78716.28643
LS refinement shellResolution: 1.542→1.582 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 25 -
Rwork0.231 606 -
obs--86.08 %

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