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- PDB-1oz3: Crystal Structure of 3-MBT repeats of lethal (3) malignant Brain ... -

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Basic information

Entry
Database: PDB / ID: 1oz3
TitleCrystal Structure of 3-MBT repeats of lethal (3) malignant Brain Tumor (Native-I) at 1.85 angstrom
ComponentsLethal(3)malignant brain tumor-like protein
KeywordsTRANSCRIPTION / Propeller / three malignant brain tumor
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
Lethal(3)malignant brain tumor-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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: Refinement description / 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_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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
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

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Assembly

Deposited unit
A: Lethal(3)malignant brain tumor-like protein
B: Lethal(3)malignant brain tumor-like protein
C: Lethal(3)malignant brain tumor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,26319
Polymers114,1313
Non-polymers2,13216
Water8,557475
1
A: Lethal(3)malignant brain tumor-like protein
B: Lethal(3)malignant brain tumor-like protein
C: Lethal(3)malignant brain tumor-like protein
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)348,79057
Polymers342,3949
Non-polymers6,39648
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z+2/31
crystal symmetry operation3_555-x+y,-x,z+1/31
Unit cell
Length a, b, c (Å)105.255, 105.255, 90.486
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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: 38043.758 Da / Num. of mol.: 3 / 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.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
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
30.15 mMammonium sulfate1reservoir
420 %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 / Date: Oct 25, 2002 / 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: 1.85→20 Å / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.478 / Num. unique all: 8263
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 112768 / % possible obs: 99.9 %
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 8263

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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: 1.85→19.84 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.239 / SU ML: 0.099 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.15 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24494 4822 5 %RANDOM
Rwork0.21086 ---
obs0.21255 90778 99.99 %-
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: 24.243 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7635 0 122 475 8232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0218043
X-RAY DIFFRACTIONr_bond_other_d0.0030.026717
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.92310995
X-RAY DIFFRACTIONr_angle_other_deg0.978315765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4955936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028892
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021662
X-RAY DIFFRACTIONr_nbd_refined0.2170.21552
X-RAY DIFFRACTIONr_nbd_other0.2640.27511
X-RAY DIFFRACTIONr_nbtor_other0.090.24093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2350
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3830.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3720.2153
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3590.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8841.54731
X-RAY DIFFRACTIONr_mcangle_it1.627686
X-RAY DIFFRACTIONr_scbond_it2.67733312
X-RAY DIFFRACTIONr_scangle_it3.8394.53309
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 350
Rwork0.261 6620
Refinement TLS params.Method: refined / Origin x: 5.764 Å / Origin y: 31.465 Å / Origin z: 7.715 Å
111213212223313233
T0.0177 Å2-0.0156 Å20.0009 Å2-0.0203 Å20.0103 Å2--0.019 Å2
L0.2407 °2-0.0858 °2-0.0225 °2-0.1148 °20.0362 °2--0.0101 °2
S-0.0024 Å °-0.0121 Å °-0.0219 Å °0.0221 Å °-0.0074 Å °0.0585 Å °0.011 Å °-0.0362 Å °0.0097 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1023 - 1211
2X-RAY DIFFRACTION1C1013 - 1126
3X-RAY DIFFRACTION1A1033 - 1204
4X-RAY DIFFRACTION1B1001 - 1022
5X-RAY DIFFRACTION1C1004 - 1012
6X-RAY DIFFRACTION1A1002 - 1032
7X-RAY DIFFRACTION1B206 - 518
8X-RAY DIFFRACTION1C206 - 518
9X-RAY DIFFRACTION1A206 - 518
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.9 Å

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