[English] 日本語
Yorodumi
- PDB-5bsj: Crystal structure of S63A mutant of human macrophage migration in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bsj
TitleCrystal structure of S63A mutant of human macrophage migration inhibitory factor
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / surface / mutation
Function / homology
Function and homology information


: / positive regulation of myeloid leukocyte cytokine production involved in immune response / negative regulation of myeloid cell apoptotic process / phenylpyruvate tautomerase / L-dopachrome isomerase / regulation of macrophage activation / dopachrome isomerase activity / phenylpyruvate tautomerase activity / cytokine receptor binding / negative regulation of mature B cell apoptotic process ...: / positive regulation of myeloid leukocyte cytokine production involved in immune response / negative regulation of myeloid cell apoptotic process / phenylpyruvate tautomerase / L-dopachrome isomerase / regulation of macrophage activation / dopachrome isomerase activity / phenylpyruvate tautomerase activity / cytokine receptor binding / negative regulation of mature B cell apoptotic process / negative regulation of macrophage chemotaxis / carboxylic acid metabolic process / positive regulation of arachidonate secretion / positive regulation of lipopolysaccharide-mediated signaling pathway / prostaglandin biosynthetic process / negative regulation of protein metabolic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of cellular senescence / positive regulation of cAMP/PKA signal transduction / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein homotrimerization / chemoattractant activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of phosphorylation / positive regulation of B cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of cell migration / positive regulation of fibroblast proliferation / cytokine activity / positive regulation of cytokine production / Cell surface interactions at the vascular wall / positive regulation of tumor necrosis factor production / protease binding / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / Neutrophil degranulation / cell surface / : / extracellular exosome / extracellular region / 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
ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPantouris, G. / Lolis, E.
CitationJournal: To Be Published
Title: Crystal structure of S63A mutant of human macrophage migration inhibitory factor
Authors: Pantouris, G. / Lolis, E.
History
DepositionJun 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
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)37,79812
Polymers37,0173
Non-polymers7819
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-83 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.785, 95.785, 103.889
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 114
2010B1 - 114
1020A1 - 114
2020C1 - 114
1030B1 - 114
2030C1 - 114

NCS ensembles :
ID
1
2
3

-
Components

#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: 12339.056 Da / Num. of mol.: 3 / Mutation: S63A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIF, GLIF, MMIF / Production host: Escherichia coli (E. coli)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 M ammonium sulfate, 3% 2-propanol, 0.1 M Tris-HCl, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 37683 / % possible obs: 99.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.023 / Rrim(I) all: 0.057 / Χ2: 0.871 / Net I/av σ(I): 24.524 / Net I/σ(I): 17.5 / Num. measured all: 218068
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.035.10.0918130.9910.0440.10.65898.8
2.03-2.075.40.08118530.9930.0380.090.66100
2.07-2.115.60.08118780.9940.0370.0890.723100
2.11-2.155.70.07718600.9920.0350.0850.77100
2.15-2.25.80.07818710.9940.0350.0860.835100
2.2-2.255.90.07218460.9950.0320.0790.758100
2.25-2.3160.0718820.9940.0310.0770.787100
2.31-2.3760.06818650.9850.030.0750.968100
2.37-2.446.10.06318700.9930.0280.070.81100
2.44-2.5260.06118940.9960.0260.0670.769100
2.52-2.6160.06218750.9960.0270.0680.938100
2.61-2.7160.05818720.9950.0250.0630.93100
2.71-2.8460.05218680.9970.0220.0570.801100
2.84-2.9960.05518940.9960.0230.060.989100
2.99-3.1760.05718770.9950.0250.0631.18699.9
3.17-3.425.90.04819090.9950.0210.0530.94100
3.42-3.765.90.04518960.9970.0190.0490.92199.9
3.76-4.315.80.04619190.9940.0190.050.98299.8
4.31-5.435.60.04819360.9940.020.0521.0899.8
5.43-5050.04120050.9970.020.0460.82998.5

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DJH

3djh


Resolution: 2→47.89 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2105 1812 4.8 %RANDOM
Rwork0.1832 ---
obs0.1845 35797 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.34 Å2 / Biso mean: 22.824 Å2 / Biso min: 12.08 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 46 169 2740
Biso mean--37.73 31.35 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192659
X-RAY DIFFRACTIONr_bond_other_d00.022496
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.9763620
X-RAY DIFFRACTIONr_angle_other_deg4.3063.0075720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7185341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.68924.804102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42315387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.754159
X-RAY DIFFRACTIONr_chiral_restr0.1280.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213026
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02591
X-RAY DIFFRACTIONr_mcbond_it2.1532.1081367
X-RAY DIFFRACTIONr_mcbond_other2.1532.1071366
X-RAY DIFFRACTIONr_mcangle_it2.593.1471704
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A117640.12
12B117640.12
21A117840.15
22C117840.15
31B119160.12
32C119160.12
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 128 -
Rwork0.187 2550 -
all-2678 -
obs--98.31 %

+
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