[English] 日本語
Yorodumi
- PDB-4k9g: 1.55 A Crystal Structure of Macrophage Migration Inhibitory Facto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k9g
Title1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor bound to ISO-66 and a related compound
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / cytokine / secreted/endocytosed
Function / homology
Function and homology information


positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process / negative regulation of mature B cell apoptotic process / negative regulation of macrophage chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / prostaglandin biosynthetic process / carboxylic acid metabolic process / regulation of macrophage activation / negative regulation of protein 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 cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / positive regulation of B cell proliferation / positive regulation of phosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of cell migration / cytokine activity / positive regulation of cytokine production / Cell surface interactions at the vascular wall / positive regulation of fibroblast proliferation / cellular senescence / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / vesicle / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular exosome / 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
Chem-1Q1 / Chem-1Q2 / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCrichlow, G.V. / Al-Abed, Y. / Lolis, E.J.
CitationJournal: INT J ONCOL. / Year: 2014
Title: ISO-66, a novel inhibitor of macrophage migration, shows efficacy in melanoma and colon cancer models.
Authors: Ioannou, K. / Cheng, K.F. / Crichlow, G.V. / Birmpilis, A.I. / Lolis, E.J. / Tsitsilonis, O.E. / Al-Abed, Y.
History
DepositionApr 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,32914
Polymers37,0653
Non-polymers1,26411
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-96 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.458, 95.458, 104.552
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21B
31A

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Macrophage migration inhibitory factor / / MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / ...MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / Phenylpyruvate tautomerase


Mass: 12355.056 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLIF, MIF, MMIF / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase

-
Non-polymers , 5 types, 292 molecules

#2: Chemical ChemComp-1Q2 / (4R,6Z)-6-(3-fluoro-4-hydroxyphenyl)-4-hydroxy-6-iminohexan-2-one


Mass: 239.243 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H14FNO3
#3: Chemical ChemComp-1Q1 / 1-[(5S)-3-(3-fluoro-4-hydroxyphenyl)-4,5-dihydro-1,2-oxazol-5-yl]propan-2-one


Mass: 237.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12FNO3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 1.1 mM (14 mg/ml) MIF , 10 mM inhibitor in 10% DMSO, 18 mM NaCl, 18 mM tris(hydroxymethyl)aminomethane mixed 1:1 with reservoir containing 2 M ammonium sulfate, 0.1 M tris(hydroxymethyl) ...Details: 1.1 mM (14 mg/ml) MIF , 10 mM inhibitor in 10% DMSO, 18 mM NaCl, 18 mM tris(hydroxymethyl)aminomethane mixed 1:1 with reservoir containing 2 M ammonium sulfate, 0.1 M tris(hydroxymethyl)aminomethane, 3% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.55→110 Å / Num. obs: 79934 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 23
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.25 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
CBASSdata collection
AMoREphasing
REFMAC5.4.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OOH

2ooh


Resolution: 1.55→82.76 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: REFINEMENT WAS BEGUN WITH CNS. REFMAC WAS USED IN LATER STAGES. IN ACTIVE SITE A, TWO FORMS OF THE INHIBITOR (RING-OPENED AND RING-CLOSED) WERE OBSERVED. THE LOWER OCCUPANCY FORM (RING- ...Details: REFINEMENT WAS BEGUN WITH CNS. REFMAC WAS USED IN LATER STAGES. IN ACTIVE SITE A, TWO FORMS OF THE INHIBITOR (RING-OPENED AND RING-CLOSED) WERE OBSERVED. THE LOWER OCCUPANCY FORM (RING-CLOSED) WAS OBSERVED IN MAPS OMITTING THIS INHIBITOR FORM WHEN CNS WAS USED FOR MAP CALCULATION, AND MISSING REFLECTIONS WERE NOT REPLACED BY FC. MAPS CALCULATED USING REFMAC, AS WELL AS CNS MAPS IN WHICH MISSING REFLECTIONS WERE REPLACED BY FC, DID NOT REVEAL THE LOWER OCCUPANCY INHIBITOR. TLS WAS USED IN LATER REFINEMENT STEPS. THE FINAL R-FACTORS LISTED TAKE THE TLS MODEL INTO ACCOUNT. WITHOUT TLS, R(OBS)=0.22629, R(WORK)=0.22590, R(FREE)=0.24575.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1597 -RANDOM
Rwork0.199 ---
obs0.199 78325 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.067 Å0.066 Å
Refinement stepCycle: LAST / Resolution: 1.55→82.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 79 281 2940
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.01
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.273
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.276
X-RAY DIFFRACTIONr_gen_planes_refined0.015
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 838 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Cloose positional0.375
2Bloose positional0.455
3Aloose positional0.495
1Cloose thermal3.8710
2Bloose thermal2.410
3Aloose thermal2.2810
LS refinement shellResolution: 1.55→1.59 Å
RfactorNum. reflection% reflection
Rfree0.325 129 -
Rwork0.289 --
obs--98.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.54560.42860.53110.5410.20270.8285-0.0598-0.0630.0636-0.0576-0.02530.07350.0042-0.07660.0851-0.0933-0.0264-0.0163-0.02540.01830.011725.814-38.85331.333
21.16410.19840.59860.35050.16020.7731-0.07720.08090.058-0.01910.092-0.0749-0.00170.1856-0.0148-0.1053-0.0077-0.02260.0236-0.00170.010245.811-36.54334.989
32.09330.03061.00950.43950.42421.39110.0944-0.4842-0.07290.1421-0.0338-0.02150.2853-0.2489-0.0606-0.079-0.0492-0.02320.0550.0587-0.006433.695-44.96749.41
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION1A17 - 35
3X-RAY DIFFRACTION1A37 - 114
4X-RAY DIFFRACTION2B1 - 15
5X-RAY DIFFRACTION2B17 - 35
6X-RAY DIFFRACTION2B37 - 114
7X-RAY DIFFRACTION3C1 - 15
8X-RAY DIFFRACTION3C17 - 35
9X-RAY DIFFRACTION3C37 - 114

+
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