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- PDB-2yyr: Structural analysis of PHD domain of Pygopus complexed with trime... -

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Basic information

Entry
Database: PDB / ID: 2yyr
TitleStructural analysis of PHD domain of Pygopus complexed with trimethylated histone H3 peptide
Components
  • H3K4Me3 peptide
  • Pygopus homolog 1
KeywordsMETAL BINDING PROTEIN / PHD finger / Bcl9/Lgs interactor / histone recognition / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


spermatid nucleus differentiation / Formation of the beta-catenin:TCF transactivating complex / anatomical structure development / spermatid development / protein localization to nucleus / canonical Wnt signaling pathway / hematopoietic progenitor cell differentiation / methylated histone binding / kidney development / positive regulation of transcription by RNA polymerase II ...spermatid nucleus differentiation / Formation of the beta-catenin:TCF transactivating complex / anatomical structure development / spermatid development / protein localization to nucleus / canonical Wnt signaling pathway / hematopoietic progenitor cell differentiation / methylated histone binding / kidney development / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus
Similarity search - Function
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/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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNakamura, Y. / Padmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structural analysis of PHD domain of Pygopus complexed with trimethylated histone H3 peptide
Authors: Nakamura, Y. / Umehara, T. / Padmanabhan, B. / Yokoyama, S.
History
DepositionMay 1, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pygopus homolog 1
B: Pygopus homolog 1
P: H3K4Me3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8977
Polymers15,6363
Non-polymers2624
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-32.4 kcal/mol
Surface area7710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.518, 59.518, 95.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Pygopus homolog 1


Mass: 7329.780 Da / Num. of mol.: 2 / Fragment: PHD Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCR2.1-TOPO / Production host: cell-free protein synthesis (unknown) / References: UniProt: Q9D0P5
#2: Protein/peptide H3K4Me3 peptide


Mass: 976.155 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthesized histone H3 peptide, tri-methylated at Lys4
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 298 K / Method: co-crystallization / pH: 9
Details: 1.0M Na Citrate, 0.1M LiSo4, 0.1mM ZnCl2, 50mM Tris-HCl, pH 9.0, co-crystallization, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 6486 / Num. obs: 6470 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Redundancy: 13.9 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.094
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.315 / Num. unique all: 630 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DX8

2dx8


Resolution: 2.5→19.43 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 105460.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 646 10.6 %RANDOM
Rwork0.213 ---
obs0.213 6106 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.0377 Å2 / ksol: 0.29875 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.62 Å20 Å20 Å2
2--7.62 Å20 Å2
3----15.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 4 60 1015
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.04
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 86 9.7 %
Rwork0.268 805 -
obs--87.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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