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- PDB-3q1j: Crystal structure of tudor domain 1 of human PHD finger protein 20 -

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Basic information

Entry
Database: PDB / ID: 3q1j
TitleCrystal structure of tudor domain 1 of human PHD finger protein 20
ComponentsPHD finger protein 20
KeywordsTRANSCRIPTION / tudor domain / mbt / structural genomics consortium / SGC
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 / HATs acetylate histones / chromatin organization / nuclear membrane ...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 / HATs acetylate histones / chromatin organization / nuclear membrane / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / 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, PHD-type, conserved site ...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, PHD-type, conserved site / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain 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 / molecular replacement / Resolution: 2.35 Å
AuthorsTempel, W. / Li, Z. / Wernimont, A.K. / Chao, X. / Bian, C. / Lam, R. / Crombet, L. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. ...Tempel, W. / Li, Z. / Wernimont, A.K. / Chao, X. / Bian, C. / Lam, R. / Crombet, L. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Febs Lett. / Year: 2012
Title: Crystal structures of the Tudor domains of human PHF20 reveal novel structural variations on the Royal Family of proteins.
Authors: Adams-Cioaba, M.A. / Li, Z. / Tempel, W. / Guo, Y. / Bian, C. / Li, Y. / Lam, R. / Min, J.
History
DepositionDec 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 9, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHD finger protein 20


Theoretical massNumber of molelcules
Total (without water)8,2112
Polymers8,2111
Non-polymers01
Water905
1
A: PHD finger protein 20

A: PHD finger protein 20


Theoretical massNumber of molelcules
Total (without water)16,4224
Polymers16,4222
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area800 Å2
ΔGint-7 kcal/mol
Surface area7790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.498, 41.062, 28.632
Angle α, β, γ (deg.)90.000, 110.330, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit was not experimentally determined.

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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: 8211.169 Da / Num. of mol.: 1 / Fragment: residues 1-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF20, C20orf104, GLEA2, HCA58, NZF, TZP / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli)
Strain (production host): BL21 (DE3) Codon plus RIL (Stratagene)
References: UniProt: Q9BVI0
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE INITIAL SEQUENCE OF THE PROTEIN HAS THE FOLLOWING SEQUENCE, ...THE INITIAL SEQUENCE OF THE PROTEIN HAS THE FOLLOWING SEQUENCE, MHHHHHHSSRENLYFQGMTKHPPNRRGISFEVGAQLEARDRLKNWYPAH IEDIDYEEGKVLIHFKRWNHRYDEWFCWDSPYLRPLEKIQLRKEGLHEE AUTHORS STATE THAT THE PROTEIN WAS LIKELY DEGRADED SPONTANEOUSLY PRIOR TO CRYSTALLIZATION. WITH UNCLEAR DEGRADATION SITE, THE CURRENT SEQRES REPRESENTES ONLY THE PROTEIN PORTION WITH VISIBLE ELECTRON DENSITY.

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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: 2.03 Å3/Da / Density % sol: 39.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG-3350, 0.2M ammonium acetate, 0.1M bis-tris. Prior to freezing, a cluster of thin rods was transferred to a drop of paratone oil. A fragment of the cluster was frozen in a stream of ...Details: 25% PEG-3350, 0.2M ammonium acetate, 0.1M bis-tris. Prior to freezing, a cluster of thin rods was transferred to a drop of paratone oil. A fragment of the cluster was frozen in a stream of cold nitrogen., pH 5.5, vapor diffusion, sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. obs: 2828 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Χ2: 1.927 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.35-2.433.30.6542881.6371100
2.43-2.533.40.562751.241100
2.53-2.653.50.3922851.431100
2.65-2.793.50.3342701.411199.6
2.79-2.963.50.222841.434199.6
2.96-3.193.50.1492821.81100
3.19-3.513.50.1142802.16199.6
3.51-4.013.50.0762822.306199.3
4.01-5.043.40.062872.5511100
5.04-203.30.0592953.279199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2rhu, 2eqm

2rhu

2eqm


Resolution: 2.35→19.08 Å / Cor.coef. Fo:Fc: 0.9033 / Cor.coef. Fo:Fc free: 0.8819 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0
Details: The programs molrep, chainsaw, phenix, refmac, coot and the ffas03 and molprobity servers where also used in the course of refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 131 4.67 %RANDOM
Rwork0.205 ---
obs0.2074 2804 --
Displacement parametersBiso max: 109.13 Å2 / Biso mean: 43.4265 Å2 / Biso min: 25.97 Å2
Baniso -1Baniso -2Baniso -3
1--10.0894 Å20 Å2-14.2796 Å2
2--8.2424 Å20 Å2
3---1.847 Å2
Refine analyzeLuzzati coordinate error obs: 0.307 Å
Refinement stepCycle: LAST / Resolution: 2.35→19.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms549 0 1 5 555
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1822
X-RAY DIFFRACTIONt_trig_c_planes142
X-RAY DIFFRACTIONt_gen_planes855
X-RAY DIFFRACTIONt_it57520
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion685
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6324
X-RAY DIFFRACTIONt_bond_d57520.01
X-RAY DIFFRACTIONt_angle_deg78821.04
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion15.94
LS refinement shellResolution: 2.35→2.63 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2997 45 5.58 %
Rwork0.2327 762 -
all0.2372 807 -

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