[English] 日本語
Yorodumi
- PDB-1oz3: Crystal Structure of 3-MBT repeats of lethal (3) malignant Brain ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more