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- PDB-1oz2: CRYSTAL STRUCTURE OF 3-MBT REPEATS OF LETHAL (3) MALIGNANT BRAIN ... -

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Basic information

Entry
Database: PDB / ID: 1oz2
TitleCRYSTAL STRUCTURE OF 3-MBT REPEATS OF LETHAL (3) MALIGNANT BRAIN TUMOR (NATIVE-II) AT 1.55 ANGSTROM
ComponentsLethal(3)malignant brain tumor-like protein
KeywordsTRANSCRIPTION / propeller / transcription repressor / three malignant brain tumor repeats
Function / homology
Function and homology information


SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation / heterochromatin formation ...SAM domain binding / chromatin lock complex / regulation of megakaryocyte differentiation / regulation of mitotic nuclear division / hemopoiesis / nucleosome binding / condensed chromosome / methylated histone binding / Regulation of TP53 Activity through Methylation / heterochromatin formation / 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 / : ...: / : / 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
Lethal(3)malignant brain tumor-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWang, W.K. / Tereshko, V. / Boccuni, P. / MacGrogan, D. / Nimer, S.D. / Patel, D.J.
CitationJournal: Structure / Year: 2003
Title: Malignant brain tumor repeats: a three-leaved propeller architecture with ligand/peptide binding pockets.
Authors: Wang, W.K. / Tereshko, V. / Boccuni, P. / MacGrogan, D. / Nimer, S.D. / Patel, D.J.
History
DepositionApr 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE These sequence conflicts (L320, R321 --> M320, C321) and (L332 --> M332) are noted in the ...SEQUENCE These sequence conflicts (L320, R321 --> M320, C321) and (L332 --> M332) are noted in the Swiss-Prot database entry (accession Q9Y468).

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9749
Polymers37,8091
Non-polymers1,1658
Water9,098505
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.680, 93.403, 58.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1228-

HOH

21A-1229-

HOH

31A-1240-

HOH

DetailsThe biological assembly with the symmetry related molecule is generated by the operation: -x, -y, z; x+1/2, -y+1/2, -z; -x+1/2, y+1/2, -z

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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


Mass: 37809.289 Da / Num. of mol.: 1 / Fragment: residues 197-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: brain / Gene: L3MBTL OR L3MBT OR KIAA0681 / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE(3)RP / References: UniProt: Q9Y468
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 3.13 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG MME 5000, MES, DTT, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMdithiothreitol1drop
2100 mMMES1reservoirpH6.5
30.1 mMammonium sulfate1reservoir
415 %PEG5000 MME1reservoir
510 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å
DetectorType: MARRESEARCH / Detector: CCD / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.067
Reflection shellResolution: 1.55→1.59 Å / Rmerge(I) obs: 0.572 / Num. unique all: 4700
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 65305 / % possible obs: 98.8 %
Reflection shell
*PLUS
% possible obs: 98.2 % / Num. unique obs: 4700

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Processing

Software
NameVersionClassification
REFMAC5.1.13refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OYX

1oyx


Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.25 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.074 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 3487 5.1 %RANDOM
Rwork0.18877 ---
obs0.19026 65305 98.79 %-
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: 16.962 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2622 0 68 505 3195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212787
X-RAY DIFFRACTIONr_bond_other_d0.0020.022326
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.933809
X-RAY DIFFRACTIONr_angle_other_deg0.93535467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023056
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02567
X-RAY DIFFRACTIONr_nbd_refined0.220.2535
X-RAY DIFFRACTIONr_nbd_other0.260.22659
X-RAY DIFFRACTIONr_nbtor_other0.0910.21407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2329
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1431.51633
X-RAY DIFFRACTIONr_mcangle_it2.08922652
X-RAY DIFFRACTIONr_scbond_it2.94831154
X-RAY DIFFRACTIONr_scangle_it4.4744.51157
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 250
Rwork0.226 4700
Refinement TLS params.Method: refined / Origin x: 5.613 Å / Origin y: 14.662 Å / Origin z: 18.64 Å
111213212223313233
T0.0537 Å2-0.0088 Å20.0075 Å2-0.0017 Å20.0019 Å2--0.0812 Å2
L0.6159 °20.0957 °20.1182 °2-0.2996 °20.0799 °2--0.2467 °2
S0.0235 Å °-0.0068 Å °0.0845 Å °0.0119 Å °-0.0172 Å °0.0019 Å °-0.0211 Å °0.0095 Å °-0.0063 Å °
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS

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