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- PDB-6l1i: Crystal Structure Of of PHF20L1 Tudor1 Y24W/Y29W mutant -

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Basic information

Entry
Database: PDB / ID: 6l1i
TitleCrystal Structure Of of PHF20L1 Tudor1 Y24W/Y29W mutant
ComponentsPHD finger protein 20-like protein 1
KeywordsMETAL BINDING PROTEIN / PHF20L1 / Tudor / Y24W/Y29W
Function / homology
Function and homology information


methylation-dependent protein binding / NSL complex / Formation of WDR5-containing histone-modifying complexes / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein catabolic process / regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm
Similarity search - Function
: / PHD finger protein 20-like protein 1 / PHD finger protein 20-like / Agenet domain, plant type / Tudor-like domain present in plant sequences. / PhD finger domain / mbt repeat / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain ...: / PHD finger protein 20-like protein 1 / PHD finger protein 20-like / Agenet domain, plant type / Tudor-like domain present in plant sequences. / PhD finger domain / mbt repeat / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
PHD finger protein 20-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsLv, M.Q. / Gao, J.
CitationJournal: J Phys Chem Lett / Year: 2020
Title: Conformational Selection in Ligand Recognition by the First Tudor Domain of PHF20L1.
Authors: Lv, M. / Gao, J. / Li, M. / Ma, R. / Li, F. / Liu, Y. / Liu, M. / Zhang, J. / Yao, X. / Wu, J. / Shi, Y. / Tang, Y. / Pan, Y. / Zhang, Z. / Ruan, K.
History
DepositionSep 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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
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: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9323
Polymers8,7401
Non-polymers1922
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-16 kcal/mol
Surface area4500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.124, 63.124, 26.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PHD finger protein 20-like protein 1 / Plant Homeodomain (PHD) Finger Protein 20-like 1


Mass: 8739.877 Da / Num. of mol.: 1 / Mutation: Y24W,Y29W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF20L1, CGI-72 / Production host: Escherichia coli (E. coli) / References: UniProt: A8MW92
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.78 Å3/Da / Density % sol: 30.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 4000, 0.2M Lithium Sulfate, 0.1M Tris, PH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.849→27.34 Å / Num. obs: 5374 / % possible obs: 99.52 % / Redundancy: 9.9 % / Biso Wilson estimate: 25.53 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 25
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 500

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SD4

3sd4


Resolution: 1.849→27.333 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 21.75
RfactorNum. reflection% reflection
Rfree0.2077 500 9.3 %
Rwork0.1601 --
obs0.1643 5374 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.34 Å2 / Biso mean: 27.2382 Å2 / Biso min: 16.92 Å2
Refinement stepCycle: final / Resolution: 1.849→27.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms589 0 10 64 663
Biso mean--72.6 32.04 -
Num. residues----68
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.849-2.03490.24561070.1895121199
2.0349-2.32930.2671300.16671195100
2.3293-2.93410.21211320.1851217100
2.9341-27.3330.18321310.1427125199
Refinement TLS params.Method: refined / Origin x: 23.0441 Å / Origin y: 8.3272 Å / Origin z: 0.1 Å
111213212223313233
T0.2085 Å2-0.0078 Å2-0.002 Å2-0.2074 Å20.0083 Å2--0.2327 Å2
L0.5546 °2-0.2106 °20.1615 °2-1.1544 °20.0414 °2--1.3112 °2
S0.0066 Å °-0.0173 Å °-0.0525 Å °0.0392 Å °0.0365 Å °0.1952 Å °0.0943 Å °-0.0331 Å °-0.0247 Å °
Refinement TLS groupSelection details: (chain 'B' and resid 3 through 70)

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