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- PDB-4pzo: Crystal structure of PHC3 SAM L967R -

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Basic information

Entry
Database: PDB / ID: 4pzo
TitleCrystal structure of PHC3 SAM L967R
ComponentsPolyhomeotic-like protein 3
KeywordsDNA BINDING PROTEIN / SAM domain / Polycomb group / polymer / chromatin
Function / homology
Function and homology information


PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / SUMOylation of DNA damage response and repair proteins / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / Regulation of PTEN gene transcription ...PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / SUMOylation of DNA damage response and repair proteins / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / Regulation of PTEN gene transcription / histone binding / Oxidative Stress Induced Senescence / negative regulation of DNA-templated transcription / chromatin binding / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Zinc finger, FCS-type / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / : / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...Zinc finger, FCS-type / FCS-type zinc finger superfamily / Zinc finger, FCS-type / Zinc finger FCS-type profile. / : / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Polyhomeotic-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsNanyes, D.R. / Junco, S.E. / Taylor, A.B. / Robinson, A.K. / Patterson, N.L. / Shivarajpur, A. / Halloran, J. / Hale, S.M. / Kaur, Y. / Hart, P.J. / Kim, C.A.
CitationJournal: Proteins / Year: 2014
Title: Multiple polymer architectures of human polyhomeotic homolog 3 sterile alpha motif.
Authors: Nanyes, D.R. / Junco, S.E. / Taylor, A.B. / Robinson, A.K. / Patterson, N.L. / Shivarajpur, A. / Halloran, J. / Hale, S.M. / Kaur, Y. / Hart, P.J. / Kim, C.A.
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyhomeotic-like protein 3
B: Polyhomeotic-like protein 3
C: Polyhomeotic-like protein 3
D: Polyhomeotic-like protein 3
E: Polyhomeotic-like protein 3
F: Polyhomeotic-like protein 3


Theoretical massNumber of molelcules
Total (without water)57,4206
Polymers57,4206
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Polyhomeotic-like protein 3


Theoretical massNumber of molelcules
Total (without water)9,5701
Polymers9,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Polyhomeotic-like protein 3


Theoretical massNumber of molelcules
Total (without water)9,5701
Polymers9,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Polyhomeotic-like protein 3


Theoretical massNumber of molelcules
Total (without water)9,5701
Polymers9,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Polyhomeotic-like protein 3


Theoretical massNumber of molelcules
Total (without water)9,5701
Polymers9,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: Polyhomeotic-like protein 3


Theoretical massNumber of molelcules
Total (without water)9,5701
Polymers9,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
F: Polyhomeotic-like protein 3


Theoretical massNumber of molelcules
Total (without water)9,5701
Polymers9,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.944, 51.745, 124.020
Angle α, β, γ (deg.)90.00, 119.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Polyhomeotic-like protein 3 / Early development regulatory protein 3 / Homolog of polyhomeotic 3 / hPH3


Mass: 9569.988 Da / Num. of mol.: 6 / Fragment: sterile alpha motif / Mutation: L967R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EDR3, PH3, PHC3 / Plasmid: pET-3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q8NDX5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.0 M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.25→46.64 Å / Num. obs: 32712 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 38.9 Å2 / Rsym value: 0.062 / Net I/σ(I): 9.8
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 4722 / Rsym value: 0.476 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PZN

4pzn


Resolution: 2.25→40.557 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 47.64 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.3347 2010 6.15 %random
Rwork0.2823 ---
obs0.2842 32704 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.7 Å2
Refinement stepCycle: LAST / Resolution: 2.25→40.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 0 107 3488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033441
X-RAY DIFFRACTIONf_angle_d0.5924642
X-RAY DIFFRACTIONf_dihedral_angle_d15.4371286
X-RAY DIFFRACTIONf_chiral_restr0.025524
X-RAY DIFFRACTIONf_plane_restr0.002593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2502-2.30650.38741400.33782176X-RAY DIFFRACTION94
2.3065-2.36890.37591450.33212159X-RAY DIFFRACTION94
2.3689-2.43860.37131360.32022155X-RAY DIFFRACTION94
2.4386-2.51730.36251410.32372190X-RAY DIFFRACTION94
2.5173-2.60720.31831400.30362176X-RAY DIFFRACTION94
2.6072-2.71160.32211460.30032189X-RAY DIFFRACTION94
2.7116-2.83490.31981420.2952180X-RAY DIFFRACTION94
2.8349-2.98440.34981400.30272186X-RAY DIFFRACTION94
2.9844-3.17130.32951430.27992194X-RAY DIFFRACTION94
3.1713-3.4160.33151450.27872182X-RAY DIFFRACTION94
3.416-3.75950.3271420.2692213X-RAY DIFFRACTION94
3.7595-4.3030.33411430.2562204X-RAY DIFFRACTION94
4.303-5.41910.33731430.26232210X-RAY DIFFRACTION94
5.4191-39.73550.36141510.26642278X-RAY DIFFRACTION93

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