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- PDB-5oqd: PHD2 and winged-helix domain of Polycomblike -

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Basic information

Entry
Database: PDB / ID: 5oqd
TitlePHD2 and winged-helix domain of Polycomblike
ComponentsPolycomb protein PclPolycomb-group proteins
KeywordsGENE REGULATION / Polycomblike / winged-helix domain / PHD finger domain
Function / homology
Function and homology information


ventral cord development / polytene chromosome / anterior/posterior axis specification / defense response to fungus / chromatin organization / microtubule binding / regulation of gene expression / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding ...ventral cord development / polytene chromosome / anterior/posterior axis specification / defense response to fungus / chromatin organization / microtubule binding / regulation of gene expression / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / DNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / Tudor domain / Tudor domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type ...Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / Tudor domain / Tudor domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
PHOSPHATE ION / Polycomb protein Pcl
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.447 Å
AuthorsChoi, J. / Benda, C. / Mueller, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Commission277899 Germany
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: DNA binding by PHF1 prolongs PRC2 residence time on chromatin and thereby promotes H3K27 methylation.
Authors: Choi, J. / Bachmann, A.L. / Tauscher, K. / Benda, C. / Fierz, B. / Muller, J.
History
DepositionAug 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Polycomb protein Pcl
A: Polycomb protein Pcl
C: Polycomb protein Pcl
D: Polycomb protein Pcl
E: Polycomb protein Pcl
F: Polycomb protein Pcl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,92325
Polymers152,6386
Non-polymers1,28519
Water4,143230
1
A: Polycomb protein Pcl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5713
Polymers25,4401
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polycomb protein Pcl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6955
Polymers25,4401
Non-polymers2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Polycomb protein Pcl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7906
Polymers25,4401
Non-polymers3505
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Polycomb protein Pcl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6654
Polymers25,4401
Non-polymers2263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Polycomb protein Pcl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5713
Polymers25,4401
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Polycomb protein Pcl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6334
Polymers25,4401
Non-polymers1933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)307.423, 53.119, 86.839
Angle α, β, γ (deg.)90.00, 105.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-824-

HOH

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Components

#1: Protein
Polycomb protein Pcl / Polycomb-group proteins / Polycomblike protein


Mass: 25439.695 Da / Num. of mol.: 6 / Fragment: UNP residues 491-694
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Pcl, CG5109 / Production host: Escherichia coli (E. coli) / References: UniProt: Q24459
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12.5 % PEG 3350, 50 mM Potassium Phosphate (dibasic) and 2 mM Manganese Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00005 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 2.447→83.694 Å / Num. obs: 49847 / % possible obs: 98.65 % / Redundancy: 3.4 % / Rpim(I) all: 0.03 / Net I/σ(I): 17.09
Reflection shellRpim(I) all: 0.371

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.447→83.694 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 32.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 4664 5 %
Rwork0.2365 --
obs0.2385 93323 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.447→83.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8786 0 42 230 9058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.029139
X-RAY DIFFRACTIONf_angle_d1.40612413
X-RAY DIFFRACTIONf_dihedral_angle_d14.4043180
X-RAY DIFFRACTIONf_chiral_restr0.061315
X-RAY DIFFRACTIONf_plane_restr0.0051595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.447-2.47480.41531490.34892860X-RAY DIFFRACTION93
2.4748-2.5040.32071600.35682978X-RAY DIFFRACTION97
2.504-2.53450.38611640.33563047X-RAY DIFFRACTION97
2.5345-2.56660.32691560.32852977X-RAY DIFFRACTION97
2.5666-2.60040.37641580.31323016X-RAY DIFFRACTION97
2.6004-2.6360.37391590.31333045X-RAY DIFFRACTION97
2.636-2.67370.36191530.30752980X-RAY DIFFRACTION97
2.6737-2.71360.37281530.30442910X-RAY DIFFRACTION95
2.7136-2.7560.35251530.28692991X-RAY DIFFRACTION97
2.756-2.80120.33711530.30492981X-RAY DIFFRACTION95
2.8012-2.84950.37041540.31282910X-RAY DIFFRACTION97
2.8495-2.90130.41041590.28493047X-RAY DIFFRACTION97
2.9013-2.95710.36231600.28572974X-RAY DIFFRACTION97
2.9571-3.01740.28151530.26872970X-RAY DIFFRACTION96
3.0174-3.08310.31861540.26223016X-RAY DIFFRACTION96
3.0831-3.15480.3451570.25462922X-RAY DIFFRACTION96
3.1548-3.23370.27241550.25262998X-RAY DIFFRACTION96
3.2337-3.32110.35961610.26252977X-RAY DIFFRACTION96
3.3211-3.41880.29731560.25122925X-RAY DIFFRACTION96
3.4188-3.52920.27241550.26032986X-RAY DIFFRACTION95
3.5292-3.65530.24881530.2442850X-RAY DIFFRACTION94
3.6553-3.80170.27351630.22763001X-RAY DIFFRACTION95
3.8017-3.97470.25881530.22512845X-RAY DIFFRACTION94
3.9747-4.18420.27051570.19722900X-RAY DIFFRACTION94
4.1842-4.44640.29631550.20763006X-RAY DIFFRACTION95
4.4464-4.78970.24621580.20052927X-RAY DIFFRACTION95
4.7897-5.27160.2131470.20422850X-RAY DIFFRACTION93
5.2716-6.03420.23841560.232947X-RAY DIFFRACTION95
6.0342-7.60170.29431540.24032971X-RAY DIFFRACTION96
7.6017-83.74340.20381460.18862852X-RAY DIFFRACTION93

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