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- PDB-4pzn: Crystal structure of PHC3 SAM L971E -

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Basic information

Entry
Database: PDB / ID: 4pzn
TitleCrystal structure of PHC3 SAM L971E
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 / Oxidative Stress Induced Senescence / histone binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,63910
Polymers47,3295
Non-polymers3105
Water72140
1


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


Theoretical massNumber of molelcules
Total (without water)9,5903
Polymers9,4661
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Polyhomeotic-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5282
Polymers9,4661
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Polyhomeotic-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5903
Polymers9,4661
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Polyhomeotic-like protein 3


Theoretical massNumber of molelcules
Total (without water)9,4661
Polymers9,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: Polyhomeotic-like protein 3


Theoretical massNumber of molelcules
Total (without water)9,4661
Polymers9,4661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.099, 60.746, 61.431
Angle α, β, γ (deg.)69.43, 75.88, 78.06
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 9465.790 Da / Num. of mol.: 5 / Fragment: sterile alpha motif / Mutation: L971E
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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 55% ethylene glycol, 100 mM tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→19.68 Å / Num. obs: 19834 / % possible obs: 97.8 % / Redundancy: 2 % / Biso Wilson estimate: 44.5 Å2 / Rsym value: 0.029 / Net I/σ(I): 11.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 2873 / Rsym value: 0.253 / % possible all: 97.2

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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: 1KW4

1kw4


Resolution: 2.3→19.683 Å / SU ML: 0.28 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 1998 10.08 %random
Rwork0.205 ---
obs0.2095 19816 97.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2706 0 20 40 2766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092771
X-RAY DIFFRACTIONf_angle_d1.2373740
X-RAY DIFFRACTIONf_dihedral_angle_d14.6851027
X-RAY DIFFRACTIONf_chiral_restr0.059424
X-RAY DIFFRACTIONf_plane_restr0.008480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35740.3171320.25871265X-RAY DIFFRACTION96
2.3574-2.42110.31071450.25981254X-RAY DIFFRACTION98
2.4211-2.49220.3141390.25521276X-RAY DIFFRACTION97
2.4922-2.57240.2951470.25151257X-RAY DIFFRACTION98
2.5724-2.66420.30451430.22621280X-RAY DIFFRACTION97
2.6642-2.77060.28641420.24051272X-RAY DIFFRACTION98
2.7706-2.89630.30191410.24561288X-RAY DIFFRACTION98
2.8963-3.04850.28251430.23791264X-RAY DIFFRACTION98
3.0485-3.23870.2991370.23261291X-RAY DIFFRACTION98
3.2387-3.48750.27031430.22661269X-RAY DIFFRACTION98
3.4875-3.83610.23921400.20821278X-RAY DIFFRACTION98
3.8361-4.38580.20531500.17261278X-RAY DIFFRACTION98
4.3858-5.50550.23611490.1911262X-RAY DIFFRACTION99
5.5055-19.68370.20061470.16121284X-RAY DIFFRACTION98

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