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- PDB-1gcz: MACROPHAGE MIGRATION INHIBITORY FACTOR (MIF) COMPLEXED WITH INHIBITOR. -

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Basic information

Entry
Database: PDB / ID: 1gcz
TitleMACROPHAGE MIGRATION INHIBITORY FACTOR (MIF) COMPLEXED WITH INHIBITOR.
ComponentsMACROPHAGE MIGRATION INHIBITORY FACTOR
KeywordsIMMUNE SYSTEM / PROTEIN-INHIBITOR COMPLEX / MIF / MACROPHAGE MIGRATION INHIBITORY FACTOR
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 / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of arachidonate secretion / cytokine receptor binding / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis ...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 / phenylpyruvate tautomerase activity / positive regulation of arachidonate secretion / cytokine receptor binding / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / carboxylic acid metabolic process / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / prostaglandin biosynthetic process / negative regulation of protein metabolic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of macrophage activation / chemoattractant activity / protein homotrimerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of cAMP/PKA signal transduction / negative regulation of cellular senescence / 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 cytokine production / cytokine activity / Cell surface interactions at the vascular wall / DNA damage response, signal transduction by p53 class mediator / positive regulation of fibroblast proliferation / positive regulation of tumor necrosis factor production / cellular senescence / protease binding / secretory granule lumen / 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
CITRIC ACID / Chem-YZ9 / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 Å
AuthorsKatayama, N. / Kurihara, H.
CitationJournal: J.Med.Chem. / Year: 2001
Title: Coumarin and chromen-4-one analogues as tautomerase inhibitors of macrophage migration inhibitory factor: discovery and X-ray crystallography.
Authors: Orita, M. / Yamamoto, S. / Katayama, N. / Aoki, M. / Takayama, K. / Yamagiwa, Y. / Seki, N. / Suzuki, H. / Kurihara, H. / Sakashita, H. / Takeuchi, M. / Fujita, S. / Yamada, T. / Tanaka, A.
History
DepositionAug 24, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 20, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)42,51819
Polymers40,2793
Non-polymers2,24016
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-132 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.6, 67.4, 87.3
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MACROPHAGE MIGRATION INHIBITORY FACTOR / MIF


Mass: 13426.209 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P14174
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4 / Details: tautomerase inhibitor
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-YZ9 / 7-HYDROXY-2-OXO-CHROMENE-3-CARBOXYLIC ACID ETHYL ESTER


Mass: 234.205 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H10O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulfate, sodium citrate, pH 5.0, vapor diffusion/hanging drop, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mg/mlprotein1drop
214.4 mMbeta-mercaptoethanol1drop
30.1 mMPMSF1drop
4100 mMsodium citrate1drop
50.6-1.5 Mammonium sulfate1reservoir
60.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: May 25, 1999
RadiationMonochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 31955 / % possible obs: 85.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 8.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.489 / Num. unique all: 1939 / % possible all: 71.5
Reflection
*PLUS
Observed criterion σ(F): 2

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Processing

Software
NameVersionClassification
X-PLOR98.1model building
X-PLOR98.1refinement
DENZOdata reduction
CCP4data scaling
X-PLOR98.1phasing
RefinementMethod to determine structure: molecular replacement
Starting model: 1GD0

1gd0


Resolution: 1.9→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: R. A. Engh and R. Huber, Acta Cryst. Sect. A., 1991
Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2712 9.8 %RANDOM
Rwork0.199 ---
obs0.199 27784 86.6 %-
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-6 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 140 137 2949
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_improper_angle_d0.85
X-RAY DIFFRACTIONx_mcbond_it1.541.5
X-RAY DIFFRACTIONx_mcangle_it2.032
X-RAY DIFFRACTIONx_scbond_it2.912
X-RAY DIFFRACTIONx_scangle_it3.982.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 382 10 %
Rwork0.24 3455 -
obs--73.1 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 98.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 9.8 % / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.85
X-RAY DIFFRACTIONx_mcbond_it1.541.5
X-RAY DIFFRACTIONx_scbond_it2.912
X-RAY DIFFRACTIONx_mcangle_it2.032
X-RAY DIFFRACTIONx_scangle_it3.982.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.27 / % reflection Rfree: 10 % / Rfactor Rwork: 0.24

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