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

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Basic information

Entry
Database: PDB / ID: 1oyx
TitleCRYSTAL STRUCTURE OF 3-MBT REPEATS OF LETHAL (3) MALIGNANT BRAIN TUMOR (SELENO-MET) AT 1.85 ANGSTROM
ComponentsLethal(3)malignant brain tumor-like protein
KeywordsTRANSCRIPTION / propeller / transcription repressor
Function / homology
Function and homology information


SAM domain binding / chromatin lock complex / constitutive heterochromatin formation / regulation of megakaryocyte differentiation / histone H4K20me2 reader activity / regulation of mitotic nuclear division / : / hemopoiesis / nucleosome binding / condensed chromosome ...SAM domain binding / chromatin lock complex / constitutive heterochromatin formation / regulation of megakaryocyte differentiation / histone H4K20me2 reader activity / regulation of mitotic nuclear division / : / hemopoiesis / nucleosome binding / condensed chromosome / 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 / 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: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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: Lethal(3)malignant brain tumor-like protein
C: Lethal(3)malignant brain tumor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,84324
Polymers114,1313
Non-polymers2,71221
Water9,134507
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)350,52872
Polymers342,3949
Non-polymers8,13563
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)105.656, 105.656, 90.369
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsThe biological assembly is a trimer generated by the operations: -y, x-y, z+2/3, -x+y, -x, z+1/3

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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.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.75 %
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: 14-ID-B / Wavelength: 1.06334, 0.97935, 0.97914, 0.95668
DetectorDetector: CCD / Date: Sep 15, 2002 / Details: mirrors
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.063341
20.979351
30.979141
40.956681
ReflectionResolution: 1.85→20 Å / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.55 / Num. unique all: 4088
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 88637 / % possible obs: 97 %
Reflection shell
*PLUS
% possible obs: 94.2 % / Num. unique obs: 4088 / Rmerge(I) obs: 0.55

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Processing

Software
NameVersionClassification
REFMAC5.1.13refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.85→19.84 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.968 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.153 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23822 4678 5 %RANDOM
Rwork0.20698 ---
obs0.20853 88633 96.98 %-
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: 31.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å20 Å2
2--0.07 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7635 0 154 507 8296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0218084
X-RAY DIFFRACTIONr_bond_other_d0.0030.026741
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.92611054
X-RAY DIFFRACTIONr_angle_other_deg0.956315825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.21088
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028880
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021662
X-RAY DIFFRACTIONr_nbd_refined0.2140.21561
X-RAY DIFFRACTIONr_nbd_other0.2580.27614
X-RAY DIFFRACTIONr_nbtor_other0.0890.24110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2431
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3890.250
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3620.2167
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3780.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0711.54728
X-RAY DIFFRACTIONr_mcangle_it1.95427683
X-RAY DIFFRACTIONr_scbond_it2.79133356
X-RAY DIFFRACTIONr_scangle_it4.3624.53371
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
Rfree0.53 209
Rwork0.504 4088
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)
11.4428-0.23820.32011.9626-0.01651.6787-0.0887-0.05850.28680.3324-0.03160.0025-0.0903-0.18670.12030.0979-0.0385-0.02320.0969-0.01880.188-4.79215.9811.221
21.1490.2052-0.45011.21890.01541.3599-0.14790.1695-0.0999-0.08290.09580.15630.1562-0.23760.05210.0561-0.0420.0030.0983-0.00390.114837.28224.1442.816
32.40350.3678-0.6021.08460.25011.84420.0274-0.0018-0.04870.1056-0.04470.17790.1129-0.14550.01730.0533-0.00080.02690.00030.00640.1619-15.45654.6219.191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA206 - 51810 - 322
2X-RAY DIFFRACTION2BB206 - 51810 - 322
3X-RAY DIFFRACTION3CC206 - 51810 - 322
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.58
LS refinement shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.9 Å / Rfactor Rfree: 0.53

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