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- PDB-5umk: Crystal structure of H62Y mutant of human macrophage migration in... -

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Basic information

Entry
Database: PDB / ID: 5umk
TitleCrystal structure of H62Y mutant of human macrophage migration inhibitory factor
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / trimeric / mutation
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
ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsPantouris, G. / Lolis, E.
CitationJournal: Cell Chem Biol / Year: 2020
Title: Regulation of MIF Enzymatic Activity by an Allosteric Site at the Central Solvent Channel.
Authors: Pantouris, G. / Khurana, L. / Ma, A. / Skeens, E. / Reiss, K. / Batista, V.S. / Lisi, G.P. / Lolis, E.J.
History
DepositionJan 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)37,75711
Polymers37,1403
Non-polymers6178
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-58 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.106, 68.305, 86.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 114 / Label seq-ID: 1 - 114

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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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: 12380.083 Da / Num. of mol.: 3 / Mutation: H62Y
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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 42758 / % possible obs: 99.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.021 / Rrim(I) all: 0.046 / Χ2: 0.805 / Net I/σ(I): 24.6 / Num. measured all: 174731
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.73-1.762.20.06721500.9870.0520.0850.66299.5
1.76-1.792.40.0630.9850.0470.080.64699.6
1.79-1.832.60.0560.990.0390.0690.63599.6
1.83-1.8630.0530.9910.0350.0640.66699.4
1.86-1.93.40.050.9930.0310.0590.68499.6
1.9-1.953.90.0490.9940.0270.0560.70399.6
1.95-24.40.0470.9950.0250.0540.714100
2-2.054.50.0440.9960.0230.050.703100
2.05-2.114.60.0430.9960.0220.0480.73100
2.11-2.184.70.0420.9960.0210.0470.73699.9
2.18-2.264.70.0420.9960.0210.0470.79100
2.26-2.354.70.0420.9970.0210.0470.809100
2.35-2.454.60.040.9960.0210.0450.801100
2.45-2.584.70.0420.9960.0210.0470.874100
2.58-2.754.70.0410.9950.0210.0460.87499.8
2.75-2.964.70.0410.9960.020.0450.96499.8
2.96-3.264.60.0420.9950.0210.0470.97499.3
3.26-3.734.60.0390.9960.020.0440.91398.8
3.73-4.694.60.0410.9960.0210.0461.00797
4.69-504.20.0360.9970.0190.0410.78292.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-20005.8.0131data scaling
PHASER3.22phasing
REFMACrefinement
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DJH

3djh


Resolution: 1.73→48.23 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.401 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.084
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1751 2031 4.8 %RANDOM
Rwork0.1462 ---
obs0.1476 40663 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 56.54 Å2 / Biso mean: 18.917 Å2 / Biso min: 10.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.73→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 38 319 2926
Biso mean--31.41 31.66 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022699
X-RAY DIFFRACTIONr_bond_other_d0.0120.022582
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.9793661
X-RAY DIFFRACTIONr_angle_other_deg2.2293.0095930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4755339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94724.808104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.18815414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.329159
X-RAY DIFFRACTIONr_chiral_restr0.1340.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213043
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02596
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A123360.09
12B123360.09
21A124840.09
22C124840.09
31B127700.08
32C127700.08
LS refinement shellResolution: 1.726→1.771 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 130 -
Rwork0.183 2870 -
all-3000 -
obs--95.48 %

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