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- PDB-3kmj: Crystal structure of vSET under condition B -

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Basic information

Entry
Database: PDB / ID: 3kmj
TitleCrystal structure of vSET under condition B
ComponentsA612L protein
KeywordsVIRAL PROTEIN / SET domain
Function / homology
Function and homology information


histone H3K37 methyltransferase activity / methylation / identical protein binding
Similarity search - Function
Histone-lysine N-methyltransferase, H3 lysine-37 specific / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Histone H3K27 methylase
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWei, H. / Zhou, M.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Dimerization of a viral SET protein endows its function.
Authors: Wei, H. / Zhou, M.M.
History
DepositionNov 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: A612L protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7993
Polymers13,6071
Non-polymers1922
Water1,45981
1
A: A612L protein
hetero molecules

A: A612L protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5976
Polymers27,2132
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
Buried area1850 Å2
ΔGint-16 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.180, 59.180, 53.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-191-

HOH

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Components

#1: Protein A612L protein


Mass: 13606.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: O41094
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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 Å3/Da / Density % sol: 38.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.6 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 19, 2008
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 9348 / Num. obs: 9329 / % possible obs: 99.8 % / Observed criterion σ(F): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KMA

3kma


Resolution: 1.85→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.281 494 random
Rwork0.234 --
all0.26 9348 -
obs0.26 9329 -
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms903 0 10 81 994
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
LS refinement shellResolution: 1.85→1.92 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.37 51 -
Rwork0.28 --
obs-990 98.6 %

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