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- PDB-5dag: Crystal structure of PZP domain of human AF10 protein -

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Basic information

Entry
Database: PDB / ID: 5dag
TitleCrystal structure of PZP domain of human AF10 protein
ComponentsProtein AF-10
KeywordsPEPTIDE BINDING PROTEIN / PHD finger / histone tail reader / epigenetics / H3K27 recognition
Function / homology
Function and homology information


nucleosome binding / histone binding / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / : / : / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. ...: / : / : / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsChen, S. / Patel, D.J.
Funding support United States, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM079641 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA66996 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA176745 United States
STARR FoundationI5-A554 United States
Leukemia & Lymphoma SocietyLLS-SCOR 7132-08 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110174 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI118891 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007276 United States
CitationJournal: Mol.Cell / Year: 2015
Title: The PZP Domain of AF10 Senses Unmodified H3K27 to Regulate DOT1L-Mediated Methylation of H3K79.
Authors: Chen, S. / Yang, Z. / Wilkinson, A.W. / Deshpande, A.J. / Sidoli, S. / Krajewski, K. / Strahl, B.D. / Garcia, B.A. / Armstrong, S.A. / Patel, D.J. / Gozani, O.
History
DepositionAug 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 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

Downloads & links

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Assembly

Deposited unit
A: Protein AF-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3476
Polymers23,0201
Non-polymers3275
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.907, 51.907, 147.727
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Protein AF-10 / ALL1-fused gene from chromosome 10 protein


Mass: 23020.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT10, AF10 / Production host: Escherichia coli (E. coli) / References: UniProt: P55197
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Crystals were grown from a solution containing 0.1 M Tris-HCl pH 8.5, 25% PEG3350 using the hanging drop vapor diffusion method
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.283 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 22991 / % possible obs: 98.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 55

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementResolution: 1.6→32.869 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 3652 7.24 %
Rwork0.1903 --
obs0.192 -99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→32.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 0 5 108 1432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071351
X-RAY DIFFRACTIONf_angle_d1.0011825
X-RAY DIFFRACTIONf_dihedral_angle_d13.997486
X-RAY DIFFRACTIONf_chiral_restr0.046190
X-RAY DIFFRACTIONf_plane_restr0.006238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6002-1.62130.30821400.28161784X-RAY DIFFRACTION96
1.6213-1.64350.26831350.26931756X-RAY DIFFRACTION99
1.6435-1.6670.23841430.2621847X-RAY DIFFRACTION100
1.667-1.69190.2651330.24951774X-RAY DIFFRACTION100
1.6919-1.71830.28471470.2441823X-RAY DIFFRACTION100
1.7183-1.74650.24931430.21351815X-RAY DIFFRACTION100
1.7465-1.77660.25131380.2081819X-RAY DIFFRACTION100
1.7766-1.80890.24171450.20411808X-RAY DIFFRACTION100
1.8089-1.84370.23851460.20191854X-RAY DIFFRACTION100
1.8437-1.88130.19381380.20431771X-RAY DIFFRACTION100
1.8813-1.92220.27191400.19681842X-RAY DIFFRACTION100
1.9222-1.96690.27661400.20641800X-RAY DIFFRACTION100
1.9669-2.01610.21341400.1971791X-RAY DIFFRACTION100
2.0161-2.07060.21521480.19611827X-RAY DIFFRACTION100
2.0706-2.13150.20421370.19081802X-RAY DIFFRACTION100
2.1315-2.20030.22811430.18671810X-RAY DIFFRACTION100
2.2003-2.27890.21661460.19521822X-RAY DIFFRACTION100
2.2789-2.37020.19851420.19321827X-RAY DIFFRACTION100
2.3702-2.4780.19641410.19731799X-RAY DIFFRACTION100
2.478-2.60860.25271360.20121811X-RAY DIFFRACTION99
2.6086-2.7720.20221430.2011776X-RAY DIFFRACTION99
2.772-2.98580.21291410.19851796X-RAY DIFFRACTION99
2.9858-3.28610.23911410.20841802X-RAY DIFFRACTION99
3.2861-3.7610.19521340.18331786X-RAY DIFFRACTION98
3.761-4.73620.17041390.15271772X-RAY DIFFRACTION97
4.7362-32.87630.20431330.1541692X-RAY DIFFRACTION94

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