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- PDB-4x3u: Crystal structure of chromobox homolog 7 (CBX7) chromodomain with... -

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Basic information

Entry
Database: PDB / ID: 4x3u
TitleCrystal structure of chromobox homolog 7 (CBX7) chromodomain with Suramin
ComponentsChromobox protein homolog 7
KeywordsTRANSCRIPTION / CBX7 / chromodomain / suramin
Function / homology
Function and homology information


sebaceous gland development / PRC1 complex / PcG protein complex / heterochromatin / methylated histone binding / positive regulation of transcription elongation by RNA polymerase II / chromatin organization / single-stranded RNA binding / chromatin binding / negative regulation of transcription by RNA polymerase II / nucleus
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
Chem-SVR / Chromobox protein homolog 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.63 Å
AuthorsRen, C. / Zhou, M.M.
CitationJournal: Chem.Biol. / Year: 2015
Title: Small-Molecule Modulators of Methyl-Lysine Binding for the CBX7 Chromodomain.
Authors: Ren, C. / Morohashi, K. / Plotnikov, A.N. / Jakoncic, J. / Smith, S.G. / Li, J. / Zeng, L. / Rodriguez, Y. / Stojanoff, V. / Walsh, M. / Zhou, M.M.
History
DepositionDec 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_struct_oper_list
Item: _chem_comp.name / _citation.journal_id_CSD ..._chem_comp.name / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromobox protein homolog 7
B: Chromobox protein homolog 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0564
Polymers15,4622
Non-polymers2,5952
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-33 kcal/mol
Surface area7890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.700, 58.700, 89.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Chromobox protein homolog 7


Mass: 7730.877 Da / Num. of mol.: 2 / Fragment: UNP residues 7-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cbx7, D15Ertd417e / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VDS3
#2: Chemical ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID / SURAMIN


Mass: 1297.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H40N6O23S6 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris pH5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→22.68 Å / Num. obs: 20256 / % possible obs: 98.78 % / Redundancy: 18.7 % / Net I/σ(I): 48.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementResolution: 1.63→22.68 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.58 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 1016 5.1 %RANDOM
Rwork0.16012 ---
obs0.16373 18956 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.954 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.63→22.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 172 149 1267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.021160
X-RAY DIFFRACTIONr_bond_other_d0.0120.021020
X-RAY DIFFRACTIONr_angle_refined_deg3.3182.1511600
X-RAY DIFFRACTIONr_angle_other_deg1.73232343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0545107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59422.3447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13515192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.131510
X-RAY DIFFRACTIONr_chiral_restr0.7970.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.030.0211225
X-RAY DIFFRACTIONr_gen_planes_other0.0330.02297
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_restr6.13232180
X-RAY DIFFRACTIONr_sphericity_free33.744540
X-RAY DIFFRACTIONr_sphericity_bonded15.70252247
LS refinement shellResolution: 1.63→1.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 75 -
Rwork0.148 1344 -
obs--98 %

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