[English] 日本語
Yorodumi
- PDB-9f5b: Identification of zinc ions in LMO4. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f5b
TitleIdentification of zinc ions in LMO4.
ComponentsLIM domain transcription factor LMO4,LIM domain-binding protein 1
KeywordsHYDROLASE / Protease
Function / homology
Function and homology information


ventral spinal cord interneuron differentiation / regulation of cell activation / spinal cord motor neuron cell fate specification / Expression and translocation of olfactory receptors / regulation of kinase activity / spinal cord association neuron differentiation / cellular component assembly / negative regulation of erythrocyte differentiation / cerebellar Purkinje cell differentiation / positive regulation of hemoglobin biosynthetic process ...ventral spinal cord interneuron differentiation / regulation of cell activation / spinal cord motor neuron cell fate specification / Expression and translocation of olfactory receptors / regulation of kinase activity / spinal cord association neuron differentiation / cellular component assembly / negative regulation of erythrocyte differentiation / cerebellar Purkinje cell differentiation / positive regulation of hemoglobin biosynthetic process / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / epithelial structure maintenance / LIM domain binding / regulation of cell fate specification / positive regulation of kinase activity / gastrulation with mouth forming second / motor neuron axon guidance / Cardiogenesis / anterior/posterior axis specification / ventricular septum development / regulation of focal adhesion assembly / cell leading edge / somatic stem cell population maintenance / hair follicle development / negative regulation of protein-containing complex assembly / positive regulation of cell adhesion / regulation of cell migration / thymus development / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / neural tube closure / Wnt signaling pathway / RNA polymerase II transcription regulator complex / Regulation of expression of SLITs and ROBOs / neuron differentiation / transcription corepressor activity / nervous system development / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / cell adhesion / negative regulation of DNA-templated transcription / chromatin binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
: / LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile.
Similarity search - Domain/homology
LIM domain transcription factor LMO4 / LIM domain-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEl Omari, K. / Forsyth, I. / Mancini, E.J. / Wagner, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Utilizing anomalous signals for element identification in macromolecular crystallography.
Authors: El Omari, K. / Forsyth, I. / Duman, R. / Orr, C.M. / Mykhaylyk, V. / Mancini, E.J. / Wagner, A.
History
DepositionApr 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LIM domain transcription factor LMO4,LIM domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4575
Polymers20,1961
Non-polymers2624
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.816, 61.816, 93.396
Angle α, β, γ (deg.)90, 90, 120
Int Tables number149
Space group name H-MP312
Components on special symmetry positions
IDModelComponents
11A-598-

HOH

21A-618-

HOH

-
Components

#1: Protein LIM domain transcription factor LMO4,LIM domain-binding protein 1 / Breast tumor autoantigen / LIM domain only protein 4 / LMO-4 / LDB-1 / Carboxyl-terminal LIM domain- ...Breast tumor autoantigen / LIM domain only protein 4 / LMO-4 / LDB-1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / LIM domain-binding factor CLIM2 / hLdb1 / Nuclear LIM interactor


Mass: 20195.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMO4, LDB1, CLIM2 / Production host: Escherichia coli (E. coli) / References: UniProt: P61968, UniProt: Q86U70
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.25 M Sodium Malonate pH 7, 20 % v/w PEG 3350

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
1801N
2801N
3801N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I2311.2853
SYNCHROTRONDiamond I2321.2874
SYNCHROTRONDiamond I2331.3051
Detector
TypeIDDetectorDate
DECTRIS PILATUS 12M1PIXELMay 25, 2023
DECTRIS PILATUS 12M2PIXELMay 25, 2023
DECTRIS PILATUS 12M3PIXELMay 25, 2023
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
11.28531
21.28741
31.30511
Reflection

Entry-ID: 9F5B / Num. obs: 19257 / CC1/2: 1 / Redundancy: 18.8 % / % possible obs: 100 % / Resolution: 1.8→53.534 Å

Rrim(I) allDiffraction-IDNet I/σ(I)
0.11118.4
0.09219.6
0.08321.1
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.830.59630.353.081
1.8-1.830.79630.462.452
1.8-1.830.79630.610.083

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→53.534 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.222 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.119 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2335 967 5.037 %
Rwork0.1983 18231 -
all0.2 --
obs-19198 99.72 %
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 mean: 46.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.124 Å2-0.062 Å20 Å2
2---0.124 Å2-0 Å2
3---0.403 Å2
Refinement stepCycle: LAST / Resolution: 1.8→53.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 4 123 1400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121310
X-RAY DIFFRACTIONr_ext_dist_refined_b00.014747
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.8141762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.215167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.868513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11910225
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.2591063
X-RAY DIFFRACTIONr_chiral_restr0.0960.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021002
X-RAY DIFFRACTIONr_nbd_refined0.1980.2545
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2902
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2119
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.224
X-RAY DIFFRACTIONr_mcbond_it4.3054.366665
X-RAY DIFFRACTIONr_mcangle_it5.7077.786827
X-RAY DIFFRACTIONr_scbond_it5.9824.858645
X-RAY DIFFRACTIONr_scangle_it8.488.685933
X-RAY DIFFRACTIONr_lrange_it10.09167.185069
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.356890.34713180.34714130.880.89899.57540.355
1.847-1.8970.362790.32512890.32713730.8960.91499.63580.332
1.897-1.9520.309560.28912650.2913290.9150.93399.3980.289
1.952-2.0120.291680.2712340.27113050.9480.94799.77010.263
2.012-2.0780.307530.26811780.2712400.9360.94799.27420.254
2.078-2.1510.273590.26211610.26312270.9480.95299.42950.24
2.151-2.2320.267830.23610970.23811830.9520.96399.74640.21
2.232-2.3230.292620.21510610.21811260.9280.9799.73360.186
2.323-2.4260.262530.2110260.21210840.9530.97199.53870.176
2.426-2.5440.244400.20310050.20510470.9620.97499.8090.17
2.544-2.6810.301550.2059460.2110020.9590.97399.90020.166
2.681-2.8440.217450.2048840.2059300.9740.97599.89250.174
2.844-3.0390.179290.1998550.1998840.980.9761000.173
3.039-3.2820.179420.1977850.1968270.9780.9781000.174
3.282-3.5940.195420.1847300.1847720.980.9821000.168
3.594-4.0160.199300.1626540.1636840.9710.9841000.152
4.016-4.6330.175260.1465890.1476150.9840.9871000.145
4.633-5.6630.221210.1525150.1545360.9770.9871000.152
5.663-7.9650.25300.2163890.2184190.970.9761000.214
7.965-53.5340.19150.1752480.1752530.9680.9711000.195

+
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