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- PDB-3mts: Chromo Domain of Human Histone-Lysine N-Methyltransferase SUV39H1 -

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Basic information

Entry
Database: PDB / ID: 3mts
TitleChromo Domain of Human Histone-Lysine N-Methyltransferase SUV39H1
ComponentsHistone-lysine N-methyltransferase SUV39H1
KeywordsTRANSFERASE / histone methyltransferase / histone-lysine N-methyltransferase / SUV39H1 / histone H3 / tri-methylation / epigenetics / transcriptional repression / transcription regulation / chromatin / chromo domain / pre-SET domain / SET domain / post-SET domain / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


peptide deformylase / peptide deformylase activity / translation / metal ion binding
Similarity search - Function
Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLam, R. / Li, Z. / Wang, J. / Crombet, L. / Walker, J.R. / Ouyang, H. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. ...Lam, R. / Li, Z. / Wang, J. / Crombet, L. / Walker, J.R. / Ouyang, H. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2012
Title: Crystal Structure of the Human SUV39H1 Chromodomain and Its Recognition of Histone H3K9me2/3.
Authors: Wang, T. / Xu, C. / Liu, Y. / Fan, K. / Li, Z. / Sun, X. / Ouyang, H. / Zhang, X. / Zhang, J. / Li, Y. / Mackenzie, F. / Min, J. / Tu, X.
History
DepositionApr 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Jan 30, 2013Group: Database references
Revision 1.4Jan 28, 2015Group: Other
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software
Revision 1.6Sep 6, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SUV39H1
B: Histone-lysine N-methyltransferase SUV39H1
C: Histone-lysine N-methyltransferase SUV39H1


Theoretical massNumber of molelcules
Total (without water)24,3013
Polymers24,3013
Non-polymers00
Water57632
1
A: Histone-lysine N-methyltransferase SUV39H1


Theoretical massNumber of molelcules
Total (without water)8,1001
Polymers8,1001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone-lysine N-methyltransferase SUV39H1


Theoretical massNumber of molelcules
Total (without water)8,1001
Polymers8,1001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone-lysine N-methyltransferase SUV39H1


Theoretical massNumber of molelcules
Total (without water)8,1001
Polymers8,1001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.528, 99.528, 118.321
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Histone-lysine N-methyltransferase SUV39H1 / Suppressor of variegation 3-9 homolog 1 / Su(var)3-9 homolog 1 / Position-effect variegation 3-9 ...Suppressor of variegation 3-9 homolog 1 / Su(var)3-9 homolog 1 / Position-effect variegation 3-9 homolog / Histone H3-K9 methyltransferase 1 / Lysine N-methyltransferase 1A


Mass: 8100.261 Da / Num. of mol.: 3 / Fragment: Chromo domain (UNP residues 44:106)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT1A, SUV39H, SUV39H1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2
References: UniProt: O43463, histone-lysine N-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5M Na Formate, 0.1M Bis-Tris Propane pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97944 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2010 / Details: Si(111) Double Crystal Monochrometer
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 11662 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.289.30.5021100
2.28-2.379.40.3891100
2.37-2.489.40.341100
2.48-2.619.40.2451100
2.61-2.779.40.1881100
2.77-2.999.40.131100
2.99-3.299.40.0891100
3.29-3.769.30.0751100
3.76-4.749.20.051100
4.74-508.80.044199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å34.83 Å
Translation2.5 Å34.83 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.2.3phasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
Locallymodified Blu-Ice GUI interface to EPICS controldata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KNA

1kna


Resolution: 2.2→34.83 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.512 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24379 555 4.8 %RANDOM
Rwork0.20831 ---
obs0.21005 11102 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.999 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.07 Å20 Å2
2---0.15 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1565 0 0 32 1597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211605
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9522159
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9385178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70722.24789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15915299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7081519
X-RAY DIFFRACTIONr_chiral_restr0.0860.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211230
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7591.5902
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45721445
X-RAY DIFFRACTIONr_scbond_it1.9513703
X-RAY DIFFRACTIONr_scangle_it3.1614.5714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 44 -
Rwork0.244 813 -
obs--99.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.79111.1972-3.52721.6316-2.86077.1368-0.1828-0.132-0.3008-0.1537-0.0123-0.02460.44010.13210.19510.22460.01510.02920.0984-0.01780.0711-6.32620.53841.11
22.5505-0.33390.16114.9705-1.63752.915-0.12090.12340.1528-0.09480.0703-0.3903-0.06280.21970.05060.06750.00280.02250.1102-0.01550.1313.37126.91917.603
33.82811.0329-0.41963.89540.26620.0988-0.1711-0.1120.1779-0.15660.15310.34260.05530.02630.0180.19790.0126-0.01850.12920.01950.0971-6.89313.02716.814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 104
2X-RAY DIFFRACTION2B43 - 103
3X-RAY DIFFRACTION3C43 - 100

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