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- PDB-7mru: Crystal structure of S62A MIF2 mutant -

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Basic information

Entry
Database: PDB / ID: 7mru
TitleCrystal structure of S62A MIF2 mutant
ComponentsD-dopachrome decarboxylase
KeywordsCYTOKINE
Function / homology
Function and homology information


D-dopachrome decarboxylase / D-dopachrome decarboxylase activity / melanin biosynthetic process / dopachrome isomerase activity / phenylpyruvate tautomerase activity / cytokine receptor binding / negative regulation of macrophage chemotaxis / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / positive regulation of ERK1 and ERK2 cascade ...D-dopachrome decarboxylase / D-dopachrome decarboxylase activity / melanin biosynthetic process / dopachrome isomerase activity / phenylpyruvate tautomerase activity / cytokine receptor binding / negative regulation of macrophage chemotaxis / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / positive regulation of ERK1 and ERK2 cascade / extracellular space / extracellular exosome / 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) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
D-dopachrome decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsMurphy, E.L. / Manjula, R. / Murphy, J.W. / Lolis, E.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase.
Authors: Chen, E. / Reiss, K. / Shah, D. / Manjula, R. / Allen, B. / Murphy, E.L. / Murphy, J.W. / Batista, V.S. / Bhandari, V. / Lolis, E.J. / Lisi, G.P.
History
DepositionMay 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 8, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-dopachrome decarboxylase
B: D-dopachrome decarboxylase
C: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8554
Polymers37,7333
Non-polymers1221
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-33 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.748, 75.891, 103.862
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-dopachrome decarboxylase / / D-dopachrome tautomerase / Phenylpyruvate tautomerase II


Mass: 12577.526 Da / Num. of mol.: 3 / Mutation: S62A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDT / Production host: Escherichia coli (E. coli) / References: UniProt: P30046, D-dopachrome decarboxylase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 623 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 N NaCl, 25%w/v PEG 3350, 0.1 M Tris at pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.51418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.51418 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 71882 / % possible obs: 95.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.022 / Rrim(I) all: 0.062 / Χ2: 0.961 / Net I/σ(I): 11.2 / Num. measured all: 468497
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.33-1.353.70.66923500.6480.3480.7621.03363.3
1.35-1.384.10.58734360.7390.2950.6631.03592
1.38-1.44.20.51534000.8020.2550.580.97791.6
1.4-1.434.30.49834760.840.2440.5590.95593.2
1.43-1.464.40.42634840.8390.2070.4770.97392.6
1.46-1.54.50.38634790.8840.1860.4310.97594.1
1.5-1.544.70.35135350.9160.1660.3920.9794.2
1.54-1.584.70.2835740.9430.1310.3110.95894.6
1.58-1.6250.24835470.9580.1140.2750.95595.5
1.62-1.685.20.20936290.9730.0940.2310.92396.8
1.68-1.745.50.18436580.9760.0810.2020.92397.2
1.74-1.815.80.1536710.9840.0640.1640.91597.6
1.81-1.896.20.13237030.990.0550.1440.93298.5
1.89-1.996.90.09537440.9940.0370.1020.97199.3
1.99-2.117.60.07437920.9970.0280.0790.94699.8
2.11-2.278.10.06238040.9980.0230.0661.01599.9
2.27-2.58.80.05237850.9980.0180.0550.8999.9
2.5-2.879.70.04238540.9990.0140.0440.96299.9
2.87-3.6112.20.03338790.9990.010.0350.957100
3.61-5011.90.028408210.0080.0291.005100

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KAN

3kan


Resolution: 1.33→42.86 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1801 3481 4.92 %
Rwork0.1609 67302 -
obs0.1618 70783 94.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 42.13 Å2 / Biso mean: 17.2115 Å2 / Biso min: 9.79 Å2
Refinement stepCycle: final / Resolution: 1.33→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 20 632 3287
Biso mean--28.95 26.97 -
Num. residues----351
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.33-1.350.2522920.23111716180861
1.35-1.370.23191260.21812354248084
1.37-1.390.2508980.20862472257088
1.39-1.410.21931350.21182559269490
1.41-1.430.25551340.1962583271793
1.43-1.460.22091430.19322596273993
1.46-1.480.19241320.18112673280595
1.48-1.510.22461360.17942628276493
1.51-1.540.16991210.16432669279095
1.54-1.580.17231210.15062682280395
1.58-1.610.16951510.14742686283795
1.61-1.650.16721610.15072704286597
1.65-1.70.1821610.15632683284496
1.7-1.750.18281270.15762790291798
1.75-1.810.18611370.16692785292298
1.81-1.870.19361500.17342768291898
1.87-1.950.18761530.18022812296599
1.95-2.030.19791200.159128712991100
2.03-2.140.15621460.156628633009100
2.14-2.280.19391550.165228272982100
2.28-2.450.21931470.170228372984100
2.45-2.70.1971660.169828593025100
2.7-3.090.14841650.16228863051100
3.09-3.890.1581380.143229353073100
3.89-42.860.16671660.140630643230100

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