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- PDB-5epj: Crystal Structure of chromodomain of CBX7 in complex with inhibit... -

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Basic information

Entry
Database: PDB / ID: 5epj
TitleCrystal Structure of chromodomain of CBX7 in complex with inhibitor UNC3866
Components
  • Chromobox protein homolog 7
  • peptide-like inhibitor UNC3866
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / structural genomics / Structural Genomics Consortium / SGC / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
UNC3866 / Chromobox protein homolog 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsLiu, Y. / Tempel, W. / Walker, J.R. / Stuckey, J.I. / Dickson, B.M. / James, L.I. / Frye, S.V. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...Liu, Y. / Tempel, W. / Walker, J.R. / Stuckey, J.I. / Dickson, B.M. / James, L.I. / Frye, S.V. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal Structure of chromodomain of CBX7 in complex with inhibitor UNC3866
Authors: Liu, Y. / Tempel, W. / Walker, J.R. / Stuckey, J.I. / Dickson, B.M. / James, L.I. / Frye, S.V. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Refinement description
Revision 2.0Nov 27, 2019Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp / pdbx_struct_oper_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _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: peptide-like inhibitor UNC3866


Theoretical massNumber of molelcules
Total (without water)7,61215
Polymers7,6122
Non-polymers013
Water84747
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-7 kcal/mol
Surface area4430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.286, 40.286, 82.092
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Chromobox protein homolog 7


Mass: 6816.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX7 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: O95931
#2: Protein/peptide peptide-like inhibitor UNC3866


Type: Oligopeptide / Class: Inhibitor / Mass: 795.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UNC3866
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M ammonium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→36.17 Å / Num. obs: 9487 / % possible obs: 99.9 % / Redundancy: 12.4 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.011 / Rrim(I) all: 0.04 / Net I/σ(I): 51.8 / Num. measured all: 117543 / Scaling rejects: 327
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.6312.30.18713.854954480.9790.0560.19698.2
8.77-36.178.60.02386.37558810.0080.02599.8

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Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementResolution: 1.6→36.17 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.901 / SU B: 1.008 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The structure was initially solved with same diffraction data but space group setting P41. ARP/WARP was used for density improvement and automated model building. PHENIX.ELBOW/MOGUL was used ...Details: The structure was initially solved with same diffraction data but space group setting P41. ARP/WARP was used for density improvement and automated model building. PHENIX.ELBOW/MOGUL was used to generate geometry restraints for inhibitor building blocks. LIGAND was used for preparation of link restraints. Link restraints were manually modified, for example to establish planar geometry of the inhibitor's methyl ester terminus. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY. Due to lack of clear electron density for the ligand's C-terminal serine methyl ester, uncertainty remains about the orientation of the ester's carbonyl plane and the rotameric state of the hydroxymethyl side chain
RfactorNum. reflection% reflection
Rfree0.2599 671 7.1 %
Rwork0.2366 --
obs0.2382 8760 99.7 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 41.32 Å2 / Biso mean: 12.164 Å2 / Biso min: 5.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.6→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms470 0 34 48 552
Biso mean--18.61 18.96 -
Num. residues----56
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.019529
X-RAY DIFFRACTIONr_bond_other_d0.0030.02525
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.966718
X-RAY DIFFRACTIONr_angle_other_deg0.90731210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.958558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.53221.90521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3151592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.592154
X-RAY DIFFRACTIONr_chiral_restr0.0970.271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021563
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02122
X-RAY DIFFRACTIONr_mcbond_it1.211.12237
X-RAY DIFFRACTIONr_mcbond_other1.181.1234
X-RAY DIFFRACTIONr_mcangle_it1.9451.659294
LS refinement shellResolution: 1.602→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 63 -
Rwork0.128 602 -
all-665 -
obs--98.52 %

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