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- PDB-3qii: Crystal structure of tudor domain 2 of human PHD finger protein 20 -

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Basic information

Entry
Database: PDB / ID: 3qii
TitleCrystal structure of tudor domain 2 of human PHD finger protein 20
ComponentsPHD finger protein 20
KeywordsTRANSCRIPTION REGULATOR / tudor domain / phd finger / Structural Genomics / 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 / chromatin organization / HATs acetylate histones / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsLi, Z. / Tempel, W. / Wernimont, A.K. / Chao, X. / Bian, C. / Lam, R. / Crombet, L. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. ...Li, Z. / Tempel, W. / Wernimont, A.K. / Chao, X. / Bian, C. / Lam, R. / Crombet, L. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / 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
DepositionJan 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Database references
Revision 1.3Apr 11, 2012Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Sep 13, 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
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein 20


Theoretical massNumber of molelcules
Total (without water)9,8192
Polymers9,8191
Non-polymers01
Water18010
1
A: PHD finger protein 20

A: PHD finger protein 20


Theoretical massNumber of molelcules
Total (without water)19,6384
Polymers19,6382
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area690 Å2
ΔGint-10 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.683, 48.683, 96.273
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsAUTHORS STATE THAT THE BIOLOGICAL MOLECULE IS UNKNOWN.

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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: 9818.977 Da / Num. of mol.: 1
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.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG-8000, 0.2M sodium chloride, 0.1M TRIS, pH 8.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97911 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 5606 / % possible obs: 99.2 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.069 / Χ2: 1.393 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.346.40.3182371.013186.8
2.34-2.388.20.3112601.1198.5
2.38-2.439.30.372710.863199.3
2.43-2.4810.30.3342740.957199.3
2.48-2.5311.80.2862641.0291100
2.53-2.5912.50.3112830.9371100
2.59-2.6613.30.2822681.0251100
2.66-2.7313.50.2482741.1511100
2.73-2.81140.1782751.0921100
2.81-2.913.70.1662761.2091100
2.9-3140.1452791.2431100
3-3.1213.70.1142831.331100
3.12-3.2613.90.0912811.3881100
3.26-3.4413.80.0692781.3551100
3.44-3.6513.80.0642811.6421100
3.65-3.9313.20.0662862.2921100
3.93-4.33130.0572932.571100
4.33-4.9513.10.0453002.1471100
4.95-6.2412.90.0373011.2981100
6.24-5011.20.033421.379199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2o4x

2o4x


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.9 / SU B: 11.554 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. The programs buccaneer, arp/warp, coot and the ffas03 and molprobity servers were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 266 4.8 %RANDOM
Rwork0.235 ---
obs0.237 5533 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.075 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å20 Å2
2--1.81 Å20 Å2
3----3.62 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms421 0 1 10 432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022432
X-RAY DIFFRACTIONr_bond_other_d0.0020.02280
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.898586
X-RAY DIFFRACTIONr_angle_other_deg0.8333682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.279551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81724.28621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1531569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.564151
X-RAY DIFFRACTIONr_chiral_restr0.1080.265
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0295
X-RAY DIFFRACTIONr_mcbond_it0.6991.5258
X-RAY DIFFRACTIONr_mcbond_other0.1741.5104
X-RAY DIFFRACTIONr_mcangle_it1.382419
X-RAY DIFFRACTIONr_scbond_it2.5073174
X-RAY DIFFRACTIONr_scangle_it4.2084.5167
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 24 -
Rwork0.319 339 -
all-363 -
obs--94.04 %
Refinement TLS params.Method: refined / Origin x: -6.0029 Å / Origin y: 27.1772 Å / Origin z: 2.5316 Å
111213212223313233
T0.3122 Å20.021 Å2-0.0055 Å2-0.2454 Å20.016 Å2--0.1429 Å2
L4.0776 °20.6746 °21.6418 °2-2.8771 °21.8823 °2--6.074 °2
S-0.074 Å °-0.1421 Å °-0.404 Å °0.2371 Å °0.1754 Å °-0.1112 Å °0.6262 Å °0.2656 Å °-0.1015 Å °

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