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- PDB-6l0x: The First Tudor Domain of PHF20L1 -

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Basic information

Entry
Database: PDB / ID: 6l0x
TitleThe First Tudor Domain of PHF20L1
ComponentsPHD finger protein 20-like protein 1
KeywordsMETAL BINDING PROTEIN / PHF20L1 / Tudor / apo
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
CITRIC ACID / PHD finger protein 20-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 27, 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
B: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3408
Polymers17,3882
Non-polymers9536
Water3,603200
1
A: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8862
Polymers8,6941
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint1 kcal/mol
Surface area4790 Å2
MethodPISA
2
B: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4546
Polymers8,6941
Non-polymers7615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.346, 32.019, 47.350
Angle α, β, γ (deg.)84.990, 88.220, 82.840
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 8693.805 Da / Num. of mol.: 2
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-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 6000, 0.1M citric acid, PH 4.0

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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: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.3→25.32 Å / Num. obs: 29808 / % possible obs: 89.3 % / Redundancy: 3 % / Biso Wilson estimate: 14.06 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 21.2
Reflection shellResolution: 1.3→1.35 Å / Rmerge(I) obs: 0.363 / Num. unique obs: 1817 / Rsym value: 0.363

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SD4

3sd4


Resolution: 1.3→25.317 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 20.67
RfactorNum. reflection% reflection
Rfree0.1818 1495 5.02 %
Rwork0.1525 --
obs0.154 29807 82.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.57 Å2 / Biso mean: 19.8837 Å2 / Biso min: 9.56 Å2
Refinement stepCycle: final / Resolution: 1.3→25.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 64 200 1465
Biso mean--33.68 31.96 -
Num. residues----136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051303
X-RAY DIFFRACTIONf_angle_d0.9281765
X-RAY DIFFRACTIONf_chiral_restr0.094156
X-RAY DIFFRACTIONf_plane_restr0.005228
X-RAY DIFFRACTIONf_dihedral_angle_d30.748495
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.34190.2306730.1786153749
1.3419-1.38990.2201910.1792197363
1.3899-1.44550.22221230.1761244278
1.4455-1.51130.22851390.1559260483
1.5113-1.5910.20351290.1536252980
1.591-1.69060.18251730.148289393
1.6906-1.82110.2161530.1538291393
1.8211-2.00440.17191600.141286592
2.0044-2.29420.17781480.1431272587
2.2942-2.88980.18021550.1627296595
2.8898-25.30.16571510.1496286692

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