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- PDB-2pqw: Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 1... -

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Basic information

Entry
Database: PDB / ID: 2pqw
TitleCrystal structure of L3MBTL1 in complex with H4K20Me2 (residues 17-25), trigonal form
Components
  • Histone H4
  • Lethal(3)malignant brain tumor-like protein
KeywordsTRANSCRIPTION / L(3)mbt-like protein / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / heterochromatin formation / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation ...SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / heterochromatin formation / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation / chromatin organization / histone binding / regulation of cell cycle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / : / Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat ...: / : / Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / Mbt repeat / MBT repeat profile. / Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 / mbt repeat / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Lethal(3)malignant brain tumor-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAllali-Hassani, A. / Liu, Y. / Herzanych, N. / Ouyang, H. / Mackenzie, F. / Crombet, L. / Loppnau, P. / Kozieradzki, I. / Vedadi, M. / Weigelt, J. ...Allali-Hassani, A. / Liu, Y. / Herzanych, N. / Ouyang, H. / Mackenzie, F. / Crombet, L. / Loppnau, P. / Kozieradzki, I. / Vedadi, M. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: L3MBTL1 recognition of mono- and dimethylated histones.
Authors: Min, J. / Allali-Hassani, A. / Nady, N. / Qi, C. / Ouyang, H. / Liu, Y. / MacKenzie, F. / Vedadi, M. / Arrowsmith, C.H.
History
DepositionMay 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Lethal(3)malignant brain tumor-like protein
B: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5135
Polymers38,3362
Non-polymers1773
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.013, 117.013, 90.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Lethal(3)malignant brain tumor-like protein / L3 / mbt-like / L3 / mbt protein homolog / H-l3 / mbt protein / H-L3 / MBT / L3MBTL1


Mass: 37110.566 Da / Num. of mol.: 1 / Fragment: Residues 200-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL, KIAA0681, L3MBT / Plasmid: pET28A-MHL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y468
#2: Protein/peptide Histone H4


Mass: 1225.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 4.66 Å3/Da / Density % sol: 73.58 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Sodium acetate pH 4.6, 4% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 28, 2007
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→33.79 Å / Num. all: 48125 / Num. obs: 48125 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 1.4 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OZ2

1oz2


Resolution: 2→33.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.594 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22804 2430 5.1 %RANDOM
Rwork0.1949 ---
obs0.19661 45655 99.09 %-
all-45655 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2→33.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 12 281 2929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212761
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.933768
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.755324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.20723.741139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1115409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9851514
X-RAY DIFFRACTIONr_chiral_restr0.1050.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022212
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21139
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21802
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2229
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8841.51692
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39722666
X-RAY DIFFRACTIONr_scbond_it2.12231271
X-RAY DIFFRACTIONr_scangle_it3.1354.51102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 157 -
Rwork0.349 3292 -
obs--96.94 %
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)
17.66122.35162.82643.91812.679710.7192-0.22010.83930.5011-0.6555-0.06370.1574-0.8636-1.06580.2838-0.0430.2357-0.22860.2830.0973-0.0975-27.513577.7825-13.6641
28.2969-2.99670.37382.5039-0.18451.51390.07980.31220.3513-0.3848-0.2145-0.0554-0.4746-0.16840.13480.08720.07-0.08150.03530.02860.0391-12.245679.0701-1.7611
30.268-0.0424-0.37030.5520.08452.2807-0.00370.0088-0.0558-0.0229-0.04730.09960.0442-0.04650.051-0.0074-0.0041-0.00090.052-0.00330.0901-6.440361.98186.7472
40.1017-0.1798-0.00060.83950.46751.8381-0.0325-0.027-0.00940.097-0.01480.09510.0270.04660.0473-0.00360.00540.00580.07480.00740.0558-4.909764.48412.5144
510.66732.8456-5.46451.2045-0.59794.4589-0.118-1.73550.35111.0163-0.14930.4371.15431.06390.26730.21380.08570.0130.28550.11950.11373.846455.28220.6326
62.908-4.28761.30559.971-0.81653.41090.00290.12140.11470.0717-0.1393-0.3883-0.05230.56040.1364-0.076-0.0032-0.00480.10460.0080.05747.182562.55618.3489
72.4057-0.6066-1.91240.34911.07293.29890.1836-0.03230.3532-0.1365-0.0105-0.099-0.41830.1725-0.17310.0671-0.01990.01210.0086-0.00330.107-7.115779.48417.8911
83.09091.94991.30392.5182-0.19421.3525-0.10120.08790.0996-0.02440.08630.0723-0.1365-0.17840.0149-0.0828-0.00650.02060.1462-0.0720.0941-24.285171.701124.1894
92.6951.32-0.86970.6652-0.49860.5622-0.08790.0717-0.0043-0.0826-0.0064-0.0658-0.0459-0.19960.0944-0.0165-0.03240.01130.0967-0.04120.0752-19.444269.452323.518
100.7790.01960.23690.4436-0.56192.3737-0.01670.20520.0922-0.1737-0.06540.1887-0.1496-0.18130.0821-0.03280.0325-0.02260.1048-0.02450.0995-23.296277.678120.8314
113.607-4.8622.243910.1041-2.08821.93660.1531-0.463-0.12480.2745-0.35010.4565-0.1082-0.66160.1969-0.10920.01080.00790.2231-0.11970.096-31.85572.808931.1022
122.4670.28160.59143.7461-0.57312.74060.0143-0.51110.26410.4148-0.31010.1761-0.2009-0.390.2958-0.0389-0.01630.06390.128-0.13480.0419-23.507275.551236.2096
131.5287-0.3226-0.23072.35531.21032.9501-0.07790.1837-0.1895-0.037-0.11550.2333-0.1349-0.58620.1934-0.11260.0808-0.10970.209-0.01730.0511-26.237573.262-0.3926
143.2972-1.06041.20275.45533.5226.38750.10070.1477-0.26270.1179-0.19950.24570.1332-1.14190.0988-0.16110.0067-0.07040.303-0.09080.0684-31.89669.22380.1048
152.757-0.59490.45080.1837-0.4432.23480.05550.1988-0.0278-0.1486-0.12240.1675-0.1557-0.22680.0669-0.00980.0747-0.07820.1423-0.02420.0478-20.981671.0832-4.89
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA206 - 2247 - 25
2X-RAY DIFFRACTION2AA225 - 23626 - 37
3X-RAY DIFFRACTION3AA237 - 27638 - 77
4X-RAY DIFFRACTION4AA277 - 30878 - 109
5X-RAY DIFFRACTION5AA309 - 315110 - 116
6X-RAY DIFFRACTION6AA316 - 332117 - 133
7X-RAY DIFFRACTION7AA333 - 347134 - 148
8X-RAY DIFFRACTION8AA348 - 358149 - 159
9X-RAY DIFFRACTION9AA359 - 387160 - 188
10X-RAY DIFFRACTION10AA388 - 402189 - 203
11X-RAY DIFFRACTION11AA403 - 415204 - 216
12X-RAY DIFFRACTION12AA416 - 441217 - 242
13X-RAY DIFFRACTION13AA442 - 472243 - 273
14X-RAY DIFFRACTION14AA473 - 492274 - 293
15X-RAY DIFFRACTION15AA493 - 520294 - 321

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