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- PDB-1fim: MACROPHAGE MIGRATION INHIBITORY FACTOR -

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Basic information

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


response to menaquinone / Cell surface interactions at the vascular wall / brain renin-angiotensin system / positive regulation of axon regeneration / positive regulation of acute inflammatory response / drinking behavior / : / positive regulation of myeloid leukocyte cytokine production involved in immune response / hair follicle development / negative regulation of myeloid cell apoptotic process ...response to menaquinone / Cell surface interactions at the vascular wall / brain renin-angiotensin system / positive regulation of axon regeneration / positive regulation of acute inflammatory response / drinking behavior / : / positive regulation of myeloid leukocyte cytokine production involved in immune response / hair follicle development / negative regulation of myeloid cell apoptotic process / phenylpyruvate tautomerase / L-dopachrome isomerase / 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 potassium ion transport / 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 smooth muscle cell migration / Neutrophil degranulation / positive regulation of cAMP/PKA signal transduction / skin development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to vitamin E / protein homotrimerization / chemoattractant activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / response to progesterone / positive regulation of phosphorylation / positive regulation of B cell proliferation / response to mechanical stimulus / positive regulation of D-glucose import across plasma membrane / response to hormone / response to glucocorticoid / positive regulation of glycolytic process / negative regulation of cell migration / positive regulation of fibroblast proliferation / DNA damage response, signal transduction by p53 class mediator / cytokine activity / positive regulation of cytokine production / response to insulin / cellular senescence / positive regulation of immune response / cellular response to hydrogen peroxide / positive regulation of tumor necrosis factor production / response to estradiol / regulation of cell population proliferation / response to lipopolysaccharide / protease binding / spermatogenesis / cellular response to hypoxia / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / response to xenobiotic stimulus / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein-containing complex binding / cell surface / : / 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
Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSuzuki, M. / Sugimoto, H. / Nakagawa, A. / Tanaka, I.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Crystal structure of the macrophage migration inhibitory factor from rat liver.
Authors: Suzuki, M. / Sugimoto, H. / Nakagawa, A. / Tanaka, I. / Nishihira, J. / Sakai, M.
#1: Journal: J.Struct.Biol. / Year: 1995
Title: Crystallization of Rat Liver Macrophage Migration Inhibitory Factor for MAD Analysis
Authors: Sugimoto, H. / Suzuki, M. / Nakagawa, A. / Tanaka, I. / Fujinaga, M. / Nishihira, J.
History
DepositionJan 31, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MACROPHAGE MIGRATION INHIBITORY FACTOR


Theoretical massNumber of molelcules
Total (without water)12,2831
Polymers12,2831
Non-polymers00
Water00
1
A: MACROPHAGE MIGRATION INHIBITORY FACTOR

A: MACROPHAGE MIGRATION INHIBITORY FACTOR

A: MACROPHAGE MIGRATION INHIBITORY FACTOR


Theoretical massNumber of molelcules
Total (without water)36,8483
Polymers36,8483
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Unit cell
Length a, b, c (Å)61.800, 61.800, 53.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein MACROPHAGE MIGRATION INHIBITORY FACTOR


Mass: 12282.658 Da / Num. of mol.: 1 / Mutation: M2A, M101A
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONYL PROTEIN (MET 47) / Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: METHIONINE AUXOTROPIC ESCHERICHIA COLI STRAINS HARVESTED IN A MEDIUM CONTAINING SELENOMETHIONINE
Organ: LIVER / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30904
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.6 Mammonium sulfate1reservoir
20.1 MMES1reservoir
310 %dioxane1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 283 K
DetectorDate: May 18, 1995
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 5697 / % possible obs: 94.5 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.2→5 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.244 -3.59 %
Rwork0.197 --
obs0.197 5143 94.6 %
Displacement parametersBiso mean: 30.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms782 0 0 0 782
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.718
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.88
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.602
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.886
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.602

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