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- PDB-3sd4: Crystal structure of the first Tudor domain of human PHF20 -

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Basic information

Entry
Database: PDB / ID: 3sd4
TitleCrystal structure of the first Tudor domain of human PHF20
ComponentsPHD finger protein 20
KeywordsTRANSCRIPTION / Tudor Domain
Function / homology
Function and homology information


NSL complex / : / Regulation of TP53 Activity through Association with Co-factors / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / Stabilization of p53 / Regulation of TP53 Degradation / chromatin organization / HATs acetylate histones ...NSL complex / : / Regulation of TP53 Activity through Association with Co-factors / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / Stabilization of p53 / Regulation of TP53 Degradation / chromatin organization / HATs acetylate histones / nuclear membrane / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
PHD finger protein 20, AT hook / PHD finger protein 20, AT-hook / DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / PHD finger protein 20-like / PhD finger domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / Zinc finger C2H2 type domain profile. ...PHD finger protein 20, AT hook / PHD finger protein 20, AT-hook / DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / PHD finger protein 20-like / PhD finger domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / Zinc finger C2H2 type domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
PHD finger protein 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.928 Å
AuthorsCui, G. / Botuyan, M.V. / Thompson, J.R. / Mer, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: PHF20 is an effector protein of p53 double lysine methylation that stabilizes and activates p53.
Authors: Cui, G. / Park, S. / Badeaux, A.I. / Kim, D. / Lee, J. / Thompson, J.R. / Yan, F. / Kaneko, S. / Yuan, Z. / Botuyan, M.V. / Bedford, M.T. / Cheng, J.Q. / Mer, G.
History
DepositionJun 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 15, 2012Group: Database references
Revision 1.3Sep 26, 2012Group: Database references
Revision 1.4Nov 6, 2019Group: Data collection / Database references / Category: pdbx_database_related / struct_ref_seq_dif
Item: _pdbx_database_related.db_name / _struct_ref_seq_dif.details
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHD finger protein 20
B: PHD finger protein 20


Theoretical massNumber of molelcules
Total (without water)17,0752
Polymers17,0752
Non-polymers00
Water3,873215
1
A: PHD finger protein 20


Theoretical massNumber of molelcules
Total (without water)8,5381
Polymers8,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHD finger protein 20


Theoretical massNumber of molelcules
Total (without water)8,5381
Polymers8,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.746, 60.761, 37.750
Angle α, β, γ (deg.)90.00, 112.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHD finger protein 20 / / Glioma-expressed antigen 2 / Hepatocellular carcinoma-associated antigen 58 / Novel zinc finger ...Glioma-expressed antigen 2 / Hepatocellular carcinoma-associated antigen 58 / Novel zinc finger protein / Transcription factor TZP


Mass: 8537.563 Da / Num. of mol.: 2 / Fragment: FIRST TUDOR DOMAIN, UNP residues 4-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF20, C20orf104, GLEA2, HCA58, NZF, TZP / Plasmid: pTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (PLysS) / References: UniProt: Q9BVI0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 28% PEG 3000, 0.2 M ammonium acetate, 0.1 M cacodylic acid , pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.928→30.38 Å / Num. obs: 11693 / % possible obs: 98.1 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.3
Reflection shellResolution: 1.928→1.96 Å / Redundancy: 7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 7.2 / Num. unique all: 2729 / % possible all: 95.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model generated using PHYRE

Resolution: 1.928→30.38 Å / SU ML: 0.54 / σ(F): 1.37 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 558 4.77 %RANDOM
Rwork0.2291 ---
obs0.2295 11693 97.87 %-
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.363 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0455 Å20 Å20.1738 Å2
2--0.7309 Å20 Å2
3---0.3146 Å2
Refinement stepCycle: LAST / Resolution: 1.928→30.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 0 215 1405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051252
X-RAY DIFFRACTIONf_angle_d0.8771706
X-RAY DIFFRACTIONf_dihedral_angle_d14.77461
X-RAY DIFFRACTIONf_chiral_restr0.061155
X-RAY DIFFRACTIONf_plane_restr0.003224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.928-2.12180.32691350.28762729X-RAY DIFFRACTION96
2.1218-2.42870.29771350.2442751X-RAY DIFFRACTION97
2.4287-3.05950.21591520.23632779X-RAY DIFFRACTION99
3.0595-30.38430.21721360.21272876X-RAY DIFFRACTION99

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