[English] 日本語
Yorodumi
- PDB-7mru: Crystal structure of S62A MIF2 mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mru
TitleCrystal structure of S62A MIF2 mutant
ComponentsD-dopachrome decarboxylase
KeywordsCYTOKINE
Function / homology
Function and homology information


D-dopachrome decarboxylase / D-dopachrome decarboxylase activity / dopachrome isomerase activity / melanin biosynthetic process / phenylpyruvate tautomerase activity / cytokine receptor binding / negative regulation of macrophage chemotaxis / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / positive regulation of ERK1 and ERK2 cascade ...D-dopachrome decarboxylase / D-dopachrome decarboxylase activity / dopachrome isomerase activity / melanin biosynthetic process / phenylpyruvate tautomerase activity / cytokine receptor binding / negative regulation of macrophage chemotaxis / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / positive regulation of ERK1 and ERK2 cascade / extracellular space / extracellular exosome / cytoplasm
Similarity search - Function
Macrophage migration inhibitory factor, conserved site / Macrophage migration inhibitory factor family signature. / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
D-dopachrome decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsMurphy, E.L. / Manjula, R. / Murphy, J.W. / Lolis, E.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase.
Authors: Chen, E. / Reiss, K. / Shah, D. / Manjula, R. / Allen, B. / Murphy, E.L. / Murphy, J.W. / Batista, V.S. / Bhandari, V. / Lolis, E.J. / Lisi, G.P.
History
DepositionMay 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 8, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-dopachrome decarboxylase
B: D-dopachrome decarboxylase
C: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8554
Polymers37,7333
Non-polymers1221
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-33 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.748, 75.891, 103.862
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein D-dopachrome decarboxylase / D-dopachrome tautomerase / Phenylpyruvate tautomerase II


Mass: 12577.526 Da / Num. of mol.: 3 / Mutation: S62A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDT / Production host: Escherichia coli (E. coli) / References: UniProt: P30046, D-dopachrome decarboxylase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 N NaCl, 25%w/v PEG 3350, 0.1 M Tris at pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.51418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.51418 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 71882 / % possible obs: 95.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.022 / Rrim(I) all: 0.062 / Χ2: 0.961 / Net I/σ(I): 11.2 / Num. measured all: 468497
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.33-1.353.70.66923500.6480.3480.7621.03363.3
1.35-1.384.10.58734360.7390.2950.6631.03592
1.38-1.44.20.51534000.8020.2550.580.97791.6
1.4-1.434.30.49834760.840.2440.5590.95593.2
1.43-1.464.40.42634840.8390.2070.4770.97392.6
1.46-1.54.50.38634790.8840.1860.4310.97594.1
1.5-1.544.70.35135350.9160.1660.3920.9794.2
1.54-1.584.70.2835740.9430.1310.3110.95894.6
1.58-1.6250.24835470.9580.1140.2750.95595.5
1.62-1.685.20.20936290.9730.0940.2310.92396.8
1.68-1.745.50.18436580.9760.0810.2020.92397.2
1.74-1.815.80.1536710.9840.0640.1640.91597.6
1.81-1.896.20.13237030.990.0550.1440.93298.5
1.89-1.996.90.09537440.9940.0370.1020.97199.3
1.99-2.117.60.07437920.9970.0280.0790.94699.8
2.11-2.278.10.06238040.9980.0230.0661.01599.9
2.27-2.58.80.05237850.9980.0180.0550.8999.9
2.5-2.879.70.04238540.9990.0140.0440.96299.9
2.87-3.6112.20.03338790.9990.010.0350.957100
3.61-5011.90.028408210.0080.0291.005100

-
Processing

Software
NameVersionClassification
PHENIX1.18refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KAN

3kan


Resolution: 1.33→42.86 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1801 3481 4.92 %
Rwork0.1609 67302 -
obs0.1618 70783 94.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 42.13 Å2 / Biso mean: 17.2115 Å2 / Biso min: 9.79 Å2
Refinement stepCycle: final / Resolution: 1.33→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 20 632 3287
Biso mean--28.95 26.97 -
Num. residues----351
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.33-1.350.2522920.23111716180861
1.35-1.370.23191260.21812354248084
1.37-1.390.2508980.20862472257088
1.39-1.410.21931350.21182559269490
1.41-1.430.25551340.1962583271793
1.43-1.460.22091430.19322596273993
1.46-1.480.19241320.18112673280595
1.48-1.510.22461360.17942628276493
1.51-1.540.16991210.16432669279095
1.54-1.580.17231210.15062682280395
1.58-1.610.16951510.14742686283795
1.61-1.650.16721610.15072704286597
1.65-1.70.1821610.15632683284496
1.7-1.750.18281270.15762790291798
1.75-1.810.18611370.16692785292298
1.81-1.870.19361500.17342768291898
1.87-1.950.18761530.18022812296599
1.95-2.030.19791200.159128712991100
2.03-2.140.15621460.156628633009100
2.14-2.280.19391550.165228272982100
2.28-2.450.21931470.170228372984100
2.45-2.70.1971660.169828593025100
2.7-3.090.14841650.16228863051100
3.09-3.890.1581380.143229353073100
3.89-42.860.16671660.140630643230100

+
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