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- PDB-3ut1: Crystal structure of the 3-MBT repeat domain of L3MBTL3 -

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Basic information

Entry
Database: PDB / ID: 3ut1
TitleCrystal structure of the 3-MBT repeat domain of L3MBTL3
ComponentsLethal(3)malignant brain tumor-like protein 3
KeywordsTRANSCRIPTION / chromatin modification / transcription repression / MBT repeat / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


methylation-dependent protein binding / granulocyte differentiation / regulation of DNA methylation-dependent heterochromatin formation / positive regulation of ubiquitin-dependent protein catabolic process / erythrocyte maturation / macrophage differentiation / chromatin organization / histone binding / negative regulation of DNA-templated transcription / chromatin binding ...methylation-dependent protein binding / granulocyte differentiation / regulation of DNA methylation-dependent heterochromatin formation / positive regulation of ubiquitin-dependent protein catabolic process / erythrocyte maturation / macrophage differentiation / chromatin organization / histone binding / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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 / SAM domain (Sterile alpha motif) / SH3 type barrels. - #140 / SAM domain profile. / Sterile alpha motif. ...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 / SAM domain (Sterile alpha motif) / SH3 type barrels. - #140 / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
: / Lethal(3)malignant brain tumor-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsZhong, N. / Tempel, W. / Wernimont, A.K. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the 3-MBT repeat domain of L3MBTL3
Authors: Zhong, N. / Tempel, W. / Wernimont, A.K. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Brown, P.J.
History
DepositionNov 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references / Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,98319
Polymers37,4501
Non-polymers53318
Water1,36976
1
A: Lethal(3)malignant brain tumor-like protein 3
hetero molecules

A: Lethal(3)malignant brain tumor-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,96538
Polymers74,8992
Non-polymers1,06636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3010 Å2
ΔGint-82 kcal/mol
Surface area31440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.287, 70.619, 58.574
Angle α, β, γ (deg.)90.000, 119.950, 90.000
Int Tables number5
Space group name H-MC121
DetailsAS PER AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein Lethal(3)malignant brain tumor-like protein 3 / H-l(3)mbt-like protein 3 / L(3)mbt-like protein 3 / MBT-1


Mass: 37449.562 Da / Num. of mol.: 1 / Fragment: UNP residues 228-551
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: L3MBTL3, KIAA1798, MBT1 / Plasmid: BL21-V2R-pRARE2 / Production host: Escherichia coli (E. coli) / Strain (production host): pET28-SBP-TEV / References: UniProt: Q96JM7
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.3 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 27% PEG-3350, 0.1M ammonium sulfate, 0.2M cobaltous chloride, 0.1M Bis-tris, pH 5.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 20483 / % possible obs: 99.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.13 / Χ2: 1.687 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.124.50.85920311.51199.5
2.12-2.214.90.7120391.519199.7
2.21-2.315.40.62420301.715199.8
2.31-2.435.50.47920411.525199.9
2.43-2.585.50.39820251.5671100
2.58-2.785.50.27720781.5841100
2.78-3.065.60.17720521.621100
3.06-3.515.60.09920211.7171100
3.51-4.425.50.06720741.8351100
4.42-505.40.05720922.21199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: based on unpublished model of L3MBTL1, itself based on molecular replacement with coordinates from PDB entry 1OYX

1oyx


Resolution: 2.05→44.761 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.201 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.902 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. Restraints for refinement of HEPES coordinates were prepared on the PRODRG server using coordinates from PDB ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. Restraints for refinement of HEPES coordinates were prepared on the PRODRG server using coordinates from PDB entry 1cxq. COOT and the MOLPROBITY server were also used. Note by author: density at residue 373 of chain a is inconsistent with valyl type.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1028 5.027 %RANDOM
Rwork0.222 ---
obs0.224 20448 99.446 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 88.31 Å2 / Biso mean: 27.696 Å2 / Biso min: 16.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.043 Å20 Å2-1.888 Å2
2---1.478 Å20 Å2
3---0.636 Å2
Refinement stepCycle: LAST / Resolution: 2.05→44.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 32 76 2571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022591
X-RAY DIFFRACTIONr_bond_other_d0.0010.021714
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9223547
X-RAY DIFFRACTIONr_angle_other_deg0.8473.0074177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9975319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.12523.983118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14915369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.277157
X-RAY DIFFRACTIONr_chiral_restr0.0780.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212911
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.1030.331750.3041338146596.451
2.103-2.1610.366800.2961372145599.794
2.161-2.2230.292690.2481309138499.566
2.223-2.2920.328650.261277134599.777
2.292-2.3660.283530.2251245130699.387
2.366-2.4490.294640.2321205127399.686
2.449-2.5410.342600.2691159122199.836
2.541-2.6450.308540.2581116117399.744
2.645-2.7620.298550.2621056111299.91
2.762-2.8960.287570.2511016107799.629
2.896-3.0520.253450.2589901035100
3.052-3.2360.345490.21689895199.579
3.236-3.4590.235500.22184089199.888
3.459-3.7340.228470.20878783799.642
3.734-4.0870.22350.18173376999.87
4.087-4.5650.192340.15966269799.857
4.565-5.2620.19310.17158361599.837
5.262-6.4230.326240.21549552199.616
6.423-8.9910.28240.17336639199.744
8.991-44.7610.198130.2320021897.706

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