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- PDB-1muf: Structure of histone H3 K4-specific methyltransferase SET7/9 -

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Basic information

Entry
Database: PDB / ID: 1muf
TitleStructure of histone H3 K4-specific methyltransferase SET7/9
ComponentsSET9
KeywordsTRANSFERASE / SET domain / histone lysine methyltransferase / knot
Function / homology
Function and homology information


heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / PKMTs methylate histone lysines / p53 binding ...heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / PKMTs methylate histone lysines / p53 binding / chromosome / chromatin organization / response to ethanol / DNA damage response / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus
Similarity search - Function
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain ...Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / 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 / Single Sheet / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.26 Å
AuthorsJacobs, S.A. / Harp, J.M. / Devarakonda, S. / Kim, Y. / Rastinejad, F. / Khorasanizadeh, S.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The active site of the SET domain is constructed on a knot
Authors: Jacobs, S.A. / Harp, J.M. / Devarakonda, S. / Kim, Y. / Rastinejad, F. / Khorasanizadeh, S.
History
DepositionSep 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SET9


Theoretical massNumber of molelcules
Total (without water)28,9361
Polymers28,9361
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.973, 110.973, 96.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-454-

HOH

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Components

#1: Protein SET9 / histone H3 lysine 4 specific methyltransferase / SET7/9


Mass: 28936.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGex / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3000, CaCl2, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal grow
*PLUS
Temperature: 10 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
220 mMimidazole1droppH7.0
3100 mM1dropNaCl
41 mMdithiothreitol1drop
50.1 MTris-HCl1reservoirpH7.0
60.2 M1reservoirCaCl2
719 %(w/v)PEG30001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.95372,0.9791,0.97921
DetectorType: SBC-2 / Detector: CCD / Date: Aug 18, 2002 / Details: mirrors
RadiationMonochromator: double crystal Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953721
20.97911
30.979211
ReflectionResolution: 2.26→19.22 Å / Num. all: 16789 / Num. obs: 16789 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.4 Å2
Reflection shellResolution: 2.26→2.34 Å / % possible all: 52
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 30900 / % possible obs: 100 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 8.8 % / Num. unique obs: 3074 / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS1.1refinement
HKL-2000data reduction
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.26→19.22 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1918515.97 / Data cutoff high rms absF: 1918515.97 / 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
Rfree0.249 848 5.1 %RANDOM
Rwork0.229 ---
all0.229 16789 --
obs0.229 16789 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.7807 Å2 / ksol: 0.349385 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å22.87 Å20 Å2
2--2.1 Å20 Å2
3----4.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.26→19.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 0 141 2151
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d27.8
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.622
X-RAY DIFFRACTIONc_scbond_it2.662
X-RAY DIFFRACTIONc_scangle_it3.932.5
LS refinement shellResolution: 2.26→2.34 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 73 4.7 %
Rwork0.271 1473 -
obs-1546 52 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.229 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.032
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.01
LS refinement shell
*PLUS
Rfactor Rfree: 0.304 / Rfactor Rwork: 0.271

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