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- PDB-3kup: Crystal Structure of the CBX3 Chromo Shadow Domain -

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Basic information

Entry
Database: PDB / ID: 3kup
TitleCrystal Structure of the CBX3 Chromo Shadow Domain
ComponentsChromobox protein homolog 3
KeywordsTRANSCRIPTION / chromo shadow domain / Structural Genomics Consortium / SGC / Chromatin regulator / Nucleus / Phosphoprotein / Repressor / Transcription regulation
Function / homology
Function and homology information


chromatin lock complex / histone methyltransferase binding / condensed chromosome, centromeric region / nuclear inner membrane / Transcriptional Regulation by E2F6 / site of DNA damage / chromosome, centromeric region / heterochromatin / pericentric heterochromatin / heterochromatin formation ...chromatin lock complex / histone methyltransferase binding / condensed chromosome, centromeric region / nuclear inner membrane / Transcriptional Regulation by E2F6 / site of DNA damage / chromosome, centromeric region / heterochromatin / pericentric heterochromatin / heterochromatin formation / methylated histone binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription coregulator binding / RNA Polymerase I Promoter Escape / euchromatin / spindle / RNA polymerase II transcription regulator complex / rhythmic process / nuclear envelope / chromatin organization / chromosome, telomeric region / chromatin remodeling / protein domain specific binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Chromobox protein homologue 3 / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...Chromobox protein homologue 3 / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / 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
Chromobox protein homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å
AuthorsTempel, W. / Li, Z. / Li, Y. / Kozieradzki, I. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. ...Tempel, W. / Li, Z. / Li, Y. / Kozieradzki, I. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal Structure of the CBX3 Chromo Shadow Domain
Authors: Tempel, W. / Li, Z. / Li, Y. / Kozieradzki, I. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Ouyang, H.
History
DepositionNov 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromobox protein homolog 3
B: Chromobox protein homolog 3
C: Chromobox protein homolog 3
D: Chromobox protein homolog 3


Theoretical massNumber of molelcules
Total (without water)28,90510
Polymers28,9054
Non-polymers06
Water2,072115
1
A: Chromobox protein homolog 3
B: Chromobox protein homolog 3


Theoretical massNumber of molelcules
Total (without water)14,4534
Polymers14,4532
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area7120 Å2
MethodPISA
2
C: Chromobox protein homolog 3
D: Chromobox protein homolog 3


Theoretical massNumber of molelcules
Total (without water)14,4536
Polymers14,4532
Non-polymers04
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-6 kcal/mol
Surface area7010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.063, 75.936, 85.944
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Chromobox protein homolog 3 / Heterochromatin protein 1 homolog gamma / HP1 gamma / Modifier 2 protein / HECH


Mass: 7226.271 Da / Num. of mol.: 4 / Fragment: Chromo Shadow Domain (UNP residues 110-173)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX3 / Plasmid: pET28a-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)_V2R / References: UniProt: Q13185
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.6 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG1500, 0.2M sodium chloride, 0.1M HEPES, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→20 Å / Num. obs: 28867 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.07 / Χ2: 1.663 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.77-1.86.50.99713931.487199.9
1.8-1.836.70.82214341.5631100
1.83-1.876.80.7314111.611100
1.87-1.916.80.58514281.621100
1.91-1.956.80.49214261.691100
1.95-1.996.80.41914161.7111100
1.99-2.046.90.3514281.7311100
2.04-2.16.90.31414201.8651100
2.1-2.1670.23514211.8481100
2.16-2.236.90.1914231.8411100
2.23-2.3170.16314341.8461100
2.31-2.470.1414271.8131100
2.4-2.517.10.12814511.771100
2.51-2.647.10.10814391.8161100
2.64-2.817.10.08114451.7431100
2.81-3.027.10.06114521.621100
3.02-3.337.10.04914661.611100
3.33-3.817.10.03314691.4551100
3.81-4.787.10.02515001.3071100
4.78-206.70.02515841.3521100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2fmm

2fmm


Resolution: 1.77→19.546 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.21 / SU B: 2.554 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ARP/WARP, COOT and MOLPROBITY have also been used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1009 3.504 %Thin shells (SFTOOLS)
Rwork0.221 ---
obs0.222 28798 99.951 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.545 Å2
Baniso -1Baniso -2Baniso -3
1-0.355 Å20 Å20 Å2
2---0.734 Å20 Å2
3---0.379 Å2
Refinement stepCycle: LAST / Resolution: 1.77→19.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 6 115 1942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221870
X-RAY DIFFRACTIONr_bond_other_d0.0010.021293
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.982518
X-RAY DIFFRACTIONr_angle_other_deg0.90233152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.61624.61578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76815325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8761511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212079
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02368
X-RAY DIFFRACTIONr_mcbond_it1.0731.51203
X-RAY DIFFRACTIONr_mcbond_other0.241.5490
X-RAY DIFFRACTIONr_mcangle_it1.96821904
X-RAY DIFFRACTIONr_scbond_it2.8913667
X-RAY DIFFRACTIONr_scangle_it4.4034.5614
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.77-1.8160.51150.3932057207699.326
1.816-1.8650.3761060.31219292035100
1.865-1.9180.2891120.27218791991100
1.918-1.9770.256930.22118101903100
1.977-2.04100.21718651865100
2.041-2.1120.279610.20917521813100
2.112-2.1910.247770.1916791756100
2.191-2.2790.21660.18416051671100
2.279-2.3790.227540.18515641618100
2.379-2.4930.27600.19714911551100
2.493-2.6250.245650.21314221487100
2.625-2.7820.302490.20913621411100
2.782-2.9690.253370.2212821319100
2.969-3.2010.3330.22712121245100
3.201-3.4970.257680.22510921160100
3.497-3.8950.274300.21610221052100
3.895-4.4680.184310.185920951100
4.468-5.4010.259260.197784810100
5.401-7.3630.291220.309639661100
7.363-19.5460.326140.257423437100

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