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- PDB-6bg7: Crystal structure of G107A mutant of human macrophage migration i... -

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Basic information

Entry
Database: PDB / ID: 6bg7
TitleCrystal structure of G107A mutant of human macrophage migration inhibitory factor
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / surface / 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 / cytoplasm / cytosol
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: 2.54 Å
AuthorsPantouris, G. / Lolis, E.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Nanosecond Dynamics Regulate the MIF-Induced Activity of CD74.
Authors: Pantouris, G. / Ho, J. / Shah, D. / Syed, M.A. / Leng, L. / Bhandari, V. / Bucala, R. / Batista, V.S. / Loria, J.P. / Lolis, E.J.
History
DepositionOct 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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)37,85612
Polymers37,1073
Non-polymers7499
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-83 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.863, 95.863, 103.712
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
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA1 - 1121 - 112
21THRTHRBB1 - 1121 - 112
12THRTHRAA1 - 1121 - 112
22THRTHRCC1 - 1121 - 112
13ALAALABB1 - 1141 - 114
23ALAALACC1 - 1141 - 114

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: 12369.081 Da / Num. of mol.: 3 / Mutation: G107A
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.: 3 / 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.: 47 / 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: 3.71 Å3/Da / Density % sol: 66.82 %
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 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. obs: 15576 / % possible obs: 83.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.054 / Rrim(I) all: 0.099 / Χ2: 0.822 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.592.40.3847540.8120.2740.4760.76583
2.59-2.642.50.3297560.8760.220.3990.71882.9
2.64-2.692.40.3377710.8680.2360.4150.79284.1
2.69-2.752.50.2517590.9140.1730.3070.83782.7
2.75-2.812.50.2247510.9240.1520.2730.71781.6
2.81-2.872.60.27620.9390.1350.2440.72984.3
2.87-2.942.60.1927760.9360.1270.2320.71884.6
2.94-3.022.60.1467840.9550.0980.1770.66184.6
3.02-3.112.70.1327720.9560.0870.1590.785
3.11-3.212.70.1047870.9790.0670.1250.68683.8
3.21-3.332.70.1097600.9750.070.1310.79883.1
3.33-3.462.70.0837910.9870.0540.10.77884.7
3.46-3.622.70.0717690.9870.0460.0850.76584.3
3.62-3.812.60.078150.9850.0450.0840.97387.4
3.81-4.052.60.0617830.9920.0390.0731.00484.1
4.05-4.362.60.0498090.9910.0320.0590.79785.7
4.36-4.82.60.058050.9910.0320.0590.84186.6
4.8-5.492.50.057910.9850.0340.0610.7283.4
5.49-6.922.50.0638030.9740.0430.0770.97683.8
6.92-502.40.0717780.9760.0480.0861.55875.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0158refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DJH

3djh


Resolution: 2.54→47.93 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.156 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.437 / ESU R Free: 0.263
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 758 4.9 %RANDOM
Rwork0.1984 ---
obs0.1998 14698 83.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.26 Å2 / Biso mean: 35.66 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.54→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 44 48 2640
Biso mean--50.07 30.45 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192643
X-RAY DIFFRACTIONr_bond_other_d0.0030.022369
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9673601
X-RAY DIFFRACTIONr_angle_other_deg1.0723.0045490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.54724.579107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45915382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.5021511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212960
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A65180.07
12B65180.07
21A64460.07
22C64460.07
31B66140.08
32C66140.08
LS refinement shellResolution: 2.54→2.606 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 56 -
Rwork0.268 969 -
all-1025 -
obs--76.55 %

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