[English] 日本語
Yorodumi
- PDB-1mff: MACROPHAGE MIGRATION INHIBITORY FACTOR Y95F MUTANT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mff
TitleMACROPHAGE MIGRATION INHIBITORY FACTOR Y95F MUTANT
ComponentsMACROPHAGE MIGRATION INHIBITORY FACTOR
KeywordsCYTOKINE / MACROPHAGE / INFLAMMATORY RESPONSE / TAUTOMERASE
Function / homology
Function and homology information


Cell surface interactions at the vascular wall / positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / positive regulation of adaptive immune response / phenylpyruvate tautomerase activity / cytokine receptor binding / positive regulation of lipopolysaccharide-mediated signaling pathway ...Cell surface interactions at the vascular wall / positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / positive regulation of adaptive immune response / phenylpyruvate tautomerase activity / cytokine receptor binding / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of protein metabolic process / prostaglandin biosynthetic process / carboxylic acid metabolic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / protein homotrimerization / positive regulation of protein kinase A signaling / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of cellular senescence / DNA damage response, signal transduction by p53 class mediator / positive regulation of B cell proliferation / positive regulation of phosphorylation / Neutrophil degranulation / negative regulation of cell migration / cytokine activity / positive regulation of cytokine production / positive regulation of MAP kinase activity / positive regulation of fibroblast proliferation / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of tumor necrosis factor production / myelin sheath / positive regulation of peptidyl-serine phosphorylation / regulation of cell population proliferation / protease binding / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / inflammatory response / positive regulation of protein phosphorylation / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / protein-containing complex binding / negative regulation of apoptotic process / cell surface / extracellular space / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol / 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) / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTaylor, A.B. / Stamps, S.L. / Wang, S.C. / Hackert, M.L. / Whitman, C.P.
CitationJournal: Biochemistry / Year: 2000
Title: Mechanism of the phenylpyruvate tautomerase activity of macrophage migration inhibitory factor: properties of the P1G, P1A, Y95F, and N97A mutants.
Authors: Stamps, S.L. / Taylor, A.B. / Wang, S.C. / Hackert, M.L. / Whitman, C.P.
History
DepositionOct 19, 1998Processing site: BNL
Revision 1.0Jul 12, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MACROPHAGE MIGRATION INHIBITORY FACTOR
B: MACROPHAGE MIGRATION INHIBITORY FACTOR
C: MACROPHAGE MIGRATION INHIBITORY FACTOR


Theoretical massNumber of molelcules
Total (without water)37,1013
Polymers37,1013
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-37 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.160, 96.160, 88.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.01584, 0.98461, -0.17403), (-0.19132, -0.17382, -0.96601), (-0.9814, 0.01799, 0.19113)-61.49907, 40.73652, -23.46506
2given(-0.00855, -0.18498, -0.98271), (0.98437, -0.17442, 0.02427), (-0.1759, -0.96714, 0.18358)-16.28695, 68.0199, 33.14172

-
Components

#1: Protein MACROPHAGE MIGRATION INHIBITORY FACTOR / / PHENYLPYRUVATE TAUTOMERASE


Mass: 12367.024 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: MIF / Plasmid: PET11B / Gene (production host): MUMIF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P34884
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.2 Å3/Da / Density % sol: 61.1 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 mg/mlprotein1drop
220 mMTris-HCl1drop
320 mM1dropNaCl
425 %PEG80001reservoir
542 mMsodium phosphate1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1998 / Details: MSC MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→33 Å / Num. obs: 30194 / % possible obs: 95.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 27.8 Å2 / Rsym value: 0.068 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.39 / % possible all: 88.5
Reflection
*PLUS
Num. measured all: 195439 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 88.5 % / Rmerge(I) obs: 0.39

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MFI

1mfi


Resolution: 2→33 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED, REFMAC USED PRIOR TO X-PLOR
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1509 5 %RANDOM
Rwork0.191 ---
obs0.191 30194 96 %-
Displacement parametersBiso mean: 30.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-33 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 0 60 2664
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.77
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.793
X-RAY DIFFRACTIONx_mcangle_it2.825
X-RAY DIFFRACTIONx_scbond_it5.86
X-RAY DIFFRACTIONx_scangle_it8.938
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.323 153 5.5 %
Rwork0.283 2607 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETERTIP3P.TOPOLOGY
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.77

+
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