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- PDB-6l1p: Crystal structure of PHF20L1 in complex with Hit 1 -

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Basic information

Entry
Database: PDB / ID: 6l1p
TitleCrystal structure of PHF20L1 in complex with Hit 1
ComponentsPHD finger protein 20-like protein 1
KeywordsMETAL BINDING PROTEIN / PHF20L1 / Tudor / Hit1
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
4-(1-methyl-3,6-dihydro-2H-pyridin-4-yl)phenol / PHD finger protein 20-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.231 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

Downloads & links

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Assembly

Deposited unit
B: PHD finger protein 20-like protein 1
A: PHD finger protein 20-like protein 1
C: PHD finger protein 20-like protein 1
D: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,10114
Polymers34,7754
Non-polymers1,32510
Water7,026390
1
B: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9753
Polymers8,6941
Non-polymers2812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area5060 Å2
MethodPISA
2
A: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1675
Polymers8,6941
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4670 Å2
MethodPISA
3
C: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0754
Polymers8,6941
Non-polymers3813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4850 Å2
MethodPISA
4
D: PHD finger protein 20-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8832
Polymers8,6941
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.801, 52.574, 101.392
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 4
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-E3X / 4-(1-methyl-3,6-dihydro-2H-pyridin-4-yl)phenol


Mass: 189.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H15NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 38.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6M magnesium sulfate, 0.1mM MES, PH 6.5

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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: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.23→36.9 Å / Num. obs: 80879 / % possible obs: 100 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 33.5
Reflection shellResolution: 1.23→1.28 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 7.1 / Num. unique obs: 7954

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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: 1.231→36.899 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 2.06 / Phase error: 17.62
RfactorNum. reflection% reflection
Rfree0.2003 4040 5 %
Rwork0.1836 --
obs0.1844 80879 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 45.39 Å2 / Biso mean: 13.488 Å2 / Biso min: 5.65 Å2
Refinement stepCycle: final / Resolution: 1.231→36.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 88 390 2855
Biso mean--14.94 20.31 -
Num. residues----276
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.231-1.2450.20591290.1959251998
1.245-1.26020.22541430.1962641100
1.2602-1.27620.18051600.19292589100
1.2762-1.2930.21381470.18632634100
1.293-1.31070.21341590.19072564100
1.3107-1.32940.18531260.19152645100
1.3294-1.34920.18291510.18462601100
1.3492-1.37030.18511430.18462621100
1.3703-1.39280.19731340.18282641100
1.3928-1.41680.19571360.18322618100
1.4168-1.44260.20631260.17852653100
1.4426-1.47030.18211180.17782641100
1.4703-1.50030.21951570.17322602100
1.5003-1.5330.19871410.18012622100
1.533-1.56860.16591440.17252658100
1.5686-1.60780.17761530.16842624100
1.6078-1.65130.2271510.17752610100
1.6513-1.69990.18281200.17922649100
1.6999-1.75480.2265950.18642713100
1.7548-1.81750.18711510.17012632100
1.8175-1.89030.18911430.17722653100
1.8903-1.97630.18081310.18152656100
1.9763-2.08050.19771370.17952680100
2.0805-2.21080.20471340.17782675100
2.2108-2.38150.19411430.18422700100
2.3815-2.62110.2181480.19562666100
2.6211-3.00020.24051600.2042687100
3.0002-3.77930.2121220.17912771100
3.7793-36.8990.17771380.18432874100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.31870.3262-0.54441.22540.29141.69740.01180.16620.1394-0.16640.02070.101-0.2264-0.1603-0.01510.08860.0095-0.00780.0770.01170.0863-4.01238.3848-12.7915
21.2767-0.19480.25560.9436-0.08341.8849-0.0119-0.0729-0.06850.06480.00180.05930.1016-0.05880.01580.05440.00410.00320.0439-0.00140.0655-4.0484-9.366512.627
30.94510.09210.37910.70660.28111.71470.0138-0.0117-0.03240.02230.0062-0.02190.08510.1072-0.01020.04440.00220.00280.0490.00220.0609-4.0982-17.6345-12.5147
40.5572-0.1333-0.12530.96060.16282.61150.05250.030.0485-0.0758-0.0277-0.0751-0.16320.1047-0.01720.0540.00670.00670.05680.00320.075-4.009916.443612.2415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 2 through 70)B2 - 70
2X-RAY DIFFRACTION2(chain 'A' and resid 3 through 70)A3 - 70
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 70)C1 - 70
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 70)D2 - 70

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