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- PDB-5wlf: Crystal structure of the apo PPS PHD finger -

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Basic information

Entry
Database: PDB / ID: 5wlf
TitleCrystal structure of the apo PPS PHD finger
ComponentsProtein partner of snf, isoform A
KeywordsHYDROLASE / Epigenetic / PHD / Histone / trimethylated
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides / small nuclear ribonucleoprotein complex / regulation of alternative mRNA splicing, via spliceosome / helicase activity / hydrolase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily ...Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein partner of snf, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKlein, B.J. / Kutateladze, T.G.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106416 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM101664 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100907 United States
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)T32AA007464 United States
CitationJournal: Structure / Year: 2017
Title: A Unique pH-Dependent Recognition of Methylated Histone H3K4 by PPS and DIDO.
Authors: Tencer, A.H. / Gatchalian, J. / Klein, B.J. / Khan, A. / Zhang, Y. / Strahl, B.D. / van Wely, K.H.M. / Kutateladze, T.G.
History
DepositionJul 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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: Protein partner of snf, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4204
Polymers7,1971
Non-polymers2233
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, HSQC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.020, 41.060, 26.410
Angle α, β, γ (deg.)90.00, 98.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein partner of snf, isoform A


Mass: 7197.483 Da / Num. of mol.: 1 / Fragment: UNP residues 908-966
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: pps, CG6525, Dmel_CG6525 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9VG78, Hydrolases; Acting on acid anhydrides
#2: 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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


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

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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: 1.72 Å3/Da / Density % sol: 28.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 0.2 M NaCl, 25% PEG 3,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.27 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27 Å / Relative weight: 1
ReflectionResolution: 1.2→26.124 Å / Num. obs: 9642 / % possible obs: 80.1 % / Redundancy: 9.3 % / Net I/σ(I): 53.02

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
d*TREKdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L7X

4l7x


Resolution: 1.4→26.124 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1602 960 10.01 %
Rwork0.1357 --
obs0.1381 9593 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→26.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms477 0 8 64 549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006514
X-RAY DIFFRACTIONf_angle_d0.882693
X-RAY DIFFRACTIONf_dihedral_angle_d3.233312
X-RAY DIFFRACTIONf_chiral_restr0.08769
X-RAY DIFFRACTIONf_plane_restr0.00889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.47380.18981370.12791229X-RAY DIFFRACTION100
1.4738-1.56620.15761370.11921239X-RAY DIFFRACTION100
1.5662-1.68710.13111370.11211232X-RAY DIFFRACTION100
1.6871-1.85680.1581370.11871231X-RAY DIFFRACTION100
1.8568-2.12540.14031360.12911234X-RAY DIFFRACTION99
2.1254-2.67730.16611410.14621253X-RAY DIFFRACTION99
2.6773-26.12890.17271350.15691215X-RAY DIFFRACTION96

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