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- PDB-1ml9: Structure of the Neurospora SET domain protein DIM-5, a histone l... -

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Basic information

Entry
Database: PDB / ID: 1ml9
TitleStructure of the Neurospora SET domain protein DIM-5, a histone lysine methyltransferase
ComponentsHistone H3 methyltransferase DIM-5
KeywordsTRANSFERASE / DIM-5 / AdoMet-dependent Methyltransferase Histone H3 Lysine-9 Methylation
Function / homology
Function and homology information


[histone H3]-lysine9 N-trimethyltransferase / histone H3K9 trimethyltransferase activity / histone methyltransferase activity / chromosome / double-stranded DNA binding / methylation / zinc ion binding / nucleus
Similarity search - Function
: / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain ...: / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Unknown ligand / : / Histone-lysine N-methyltransferase, H3 lysine-9 specific dim-5
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å
AuthorsZhang, X. / Tamaru, H. / Khan, S.I. / Horton, J.R. / Keefe, L.J. / Selker, E.U. / Cheng, X.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase
Authors: Zhang, X. / Tamaru, H. / Khan, S.I. / Horton, J.R. / Keefe, L.J. / Selker, E.U. / Cheng, X.
History
DepositionAug 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Feb 12, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3 methyltransferase DIM-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,92610
Polymers34,1121
Non-polymers8159
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.73, 81.56, 101.27
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone H3 methyltransferase DIM-5


Mass: 34111.551 Da / Num. of mol.: 1 / Fragment: Residues 17-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Plasmid: pXC379 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: GenBank: 17063801, UniProt: Q8X225*PLUS, histone-lysine N-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Mass: 103.120 Da / Num. of mol.: 6 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 9.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110-15 mg/mlprotein1drop
220 mMglycine1droppH9.8
3150 mM1dropNaCl
41 mMdithiothreitol1drop
55 %glycerol1drop
60.600 mMAdoHcy1drop
71.1-1.2 Mammonium sulfate1reservoir
8100 mMsodium citrate1reservoirpH5.4-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0332, 1.2834, 1.2830
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 10, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
21.28341
31.2831
ReflectionResolution: 1.98→24.83 Å / Num. all: 20963 / Num. obs: 20963 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.37 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 15.4
Reflection shellResolution: 1.98→2.02 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 6.1 / Num. unique all: 1011 / Rsym value: 0.276 / % possible all: 95.8
Reflection
*PLUS
% possible obs: 97 % / Num. measured all: 112569 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 95.8 % / Rmerge(I) obs: 0.276

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
X-PLOR3.851refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.98→24.83 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2620 -RANDOM
Rwork0.205 ---
all-20963 --
obs-20963 97 %-
Displacement parametersBiso mean: 32.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 24.83 Å / Luzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.98→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 3 117 2043
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d1.5
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_improper_angle_d0.72
LS refinement shellResolution: 1.98→2.1 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.281 342 -
Rwork0.266 --
obs-4258 67.5 %
Refinement
*PLUS
Rfactor Rfree: 0.258 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.72
LS refinement shell
*PLUS
Rfactor Rfree: 0.281 / Rfactor Rwork: 0.266

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