[English] 日本語
Yorodumi
- PDB-8dqa: Structure of A. thaliana MIF/D-DT-like protein-3 (MDL3) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dqa
TitleStructure of A. thaliana MIF/D-DT-like protein-3 (MDL3)
ComponentsLS1-like protein
KeywordsCYTOKINE
Function / homologyMacrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / LS1-like protein
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsManjula, R. / Basquin, J. / Lolis, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci.Signal. / Year: 2023
Title: Plant MDL proteins synergize with the cytokine MIF at CXCR2 and CXCR4 receptors in human cells.
Authors: Spiller, L. / Manjula, R. / Leissing, F. / Basquin, J. / Bourilhon, P. / Sinitski, D. / Brandhofer, M. / Levecque, S. / Gerra, S. / Sabelleck, B. / Zhang, L. / Feederle, R. / Flatley, A. / ...Authors: Spiller, L. / Manjula, R. / Leissing, F. / Basquin, J. / Bourilhon, P. / Sinitski, D. / Brandhofer, M. / Levecque, S. / Gerra, S. / Sabelleck, B. / Zhang, L. / Feederle, R. / Flatley, A. / Hoffmann, A. / Panstruga, R. / Bernhagen, J. / Lolis, E.
History
DepositionJul 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LS1-like protein


Theoretical massNumber of molelcules
Total (without water)10,9131
Polymers10,9131
Non-polymers00
Water57632
1
A: LS1-like protein

A: LS1-like protein

A: LS1-like protein


Theoretical massNumber of molelcules
Total (without water)32,7383
Polymers32,7383
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
Buried area4060 Å2
ΔGint-19 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.499, 89.499, 89.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

-
Components

#1: Protein LS1-like protein


Mass: 10912.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: T18N14.40, At3g51660 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9SCU2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM MES, pH 6.0, 4% MPD, 0.2 M ammonium acetate, 30% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→44.75 Å / Num. obs: 8229 / % possible obs: 99.96 % / Redundancy: 12.8 % / Biso Wilson estimate: 40.22 Å2 / CC1/2: 1 / Net I/σ(I): 35.38
Reflection shellResolution: 2→2.072 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 4.35 / Num. unique obs: 804 / CC1/2: 0.923 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7MRV

7mrv


Resolution: 2→44.75 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 375 4.56 %
Rwork0.1949 --
obs0.1962 8226 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 0 32 784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002767
X-RAY DIFFRACTIONf_angle_d0.4811044
X-RAY DIFFRACTIONf_dihedral_angle_d4.059105
X-RAY DIFFRACTIONf_chiral_restr0.05128
X-RAY DIFFRACTIONf_plane_restr0.003131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.290.2941230.26912581X-RAY DIFFRACTION100
2.29-2.880.25021380.23692582X-RAY DIFFRACTION100
2.89-44.750.20671140.17142688X-RAY DIFFRACTION100

+
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