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- PDB-7mrv: F100A mutant structure of MIF2 (D-DT) -

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Basic information

Entry
Database: PDB / ID: 7mrv
TitleF100A mutant structure of MIF2 (D-DT)
ComponentsD-dopachrome decarboxylase
KeywordsCYTOKINE
Function / homology
Function and homology information


D-dopachrome decarboxylase / D-dopachrome decarboxylase activity / dopachrome isomerase activity / melanin biosynthetic process / 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 / dopachrome isomerase activity / melanin biosynthetic process / 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: 1.57 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

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Assembly

Deposited unit
A: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6132
Polymers12,5171
Non-polymers961
Water2,468137
1
A: D-dopachrome decarboxylase
hetero molecules

A: D-dopachrome decarboxylase
hetero molecules

A: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8406
Polymers37,5523
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6650 Å2
ΔGint-79 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.161, 83.161, 37.781
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 12517.430 Da / Num. of mol.: 1 / Mutation: F100A
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M Ammonium sulfate, 25% PEG3350, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.514 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 8, 2021 / Details: Osmic VariMax ArcSec Cu-HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 13566 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 13.04 Å2 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.012 / Rrim(I) all: 0.033 / Χ2: 0.83 / Net I/σ(I): 31.4 / Num. measured all: 70639
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.57-1.63.30.1296880.980.0790.1520.98198.4
1.6-1.633.70.1186590.9840.0690.1371.01399.5
1.63-1.663.80.126980.9820.0690.1390.965100
1.66-1.693.90.0916830.9890.0510.1050.88299.9
1.69-1.7340.0836700.9890.0470.0960.917100
1.73-1.774.10.0786690.9910.0430.090.833100
1.77-1.814.40.0666780.9930.0350.0750.793100
1.81-1.864.40.0556820.9960.0290.0620.812100
1.86-1.924.60.0466710.9960.0230.0510.744100
1.92-1.984.80.0397080.9970.0190.0430.731100
1.98-2.0550.0356450.9980.0170.0390.748100
2.05-2.135.20.0326860.9980.0150.0360.762100
2.13-2.235.50.0296810.9980.0130.0320.712100
2.23-2.355.70.0276830.9990.0120.030.651100
2.35-2.4960.0266790.9990.0120.0290.655100
2.49-2.686.40.0256780.9990.0110.0270.71100
2.68-2.956.80.0236750.9990.0090.0250.66100
2.95-3.3870.0246760.9990.010.0260.732100
3.38-4.266.70.0266740.9990.0110.0290.93599.7
4.26-508.90.0326830.9990.0110.0341.3100

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Processing

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

3kan


Resolution: 1.57→41.58 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 683 5.04 %
Rwork0.167 12882 -
obs0.1693 13565 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.62 Å2 / Biso mean: 14.9055 Å2 / Biso min: 4.61 Å2
Refinement stepCycle: final / Resolution: 1.57→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 0 5 137 932
Biso mean--30.43 24.5 -
Num. residues----109
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.57-1.690.26161360.20652544268098
1.69-1.860.22881420.165325732715100
1.86-2.130.20221210.175726042725100
2.13-2.680.21681160.179825992715100
2.68-41.580.19911680.14925622730100

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