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- PDB-6l1c: Crystal Structure Of of PHF20L1 Tudor1 Y24L mutant -

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Basic information

Entry
Database: PDB / ID: 6l1c
TitleCrystal Structure Of of PHF20L1 Tudor1 Y24L mutant
ComponentsPHD finger protein 20-like protein 1
KeywordsMETAL BINDING PROTEIN / PHF20L1 / Tudor / Y24L
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 / nucleoplasm / metal ion binding
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: 1.58 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 28, 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
A: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0245
Polymers8,6441
Non-polymers3804
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area4760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.570, 52.570, 38.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 8643.789 Da / Num. of mol.: 1 / Mutation: Y24L
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6M 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: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.488
ReflectionResolution: 1.58→37.173 Å / Num. obs: 13228 / % possible obs: 99.93 % / Redundancy: 13.2 % / Biso Wilson estimate: 16.48 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 37.4
Reflection shellResolution: 1.582→1.623 Å / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 6.3 / Num. unique obs: 956

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SD4

3sd4


Resolution: 1.58→37.17 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2302 / WRfactor Rwork: 0.1911 / FOM work R set: 0.9092 / SU B: 0.858 / SU ML: 0.032 / SU R Cruickshank DPI: 0.0151 / SU Rfree: 0.0145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.015 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1909 1319 9.1 %RANDOM
Rwork0.178 ---
obs0.1792 13228 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.94 Å2 / Biso mean: 16.575 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.58→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms596 0 21 35 652
Biso mean--51.95 32.78 -
Num. residues----68
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.013643
X-RAY DIFFRACTIONr_bond_other_d0.0010.017571
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.648872
X-RAY DIFFRACTIONr_angle_other_deg1.1131.5831320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.453569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.06519.77344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17915109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.015158
X-RAY DIFFRACTIONr_chiral_restr0.0490.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02159
LS refinement shellResolution: 1.582→1.623 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 102 -
Rwork0.165 956 -
all-1058 -
obs--99.62 %

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