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- PDB-7mw7: Crystal structure of P1G mutant of D-dopachrome tautomerase -

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Basic information

Entry
Database: PDB / ID: 7mw7
TitleCrystal structure of P1G mutant of D-dopachrome tautomerase
ComponentsD-dopachrome decarboxylase
KeywordsCYTOKINE / Mitogen inhibitory factor 2 / Mutant / Lyase
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: 1.1 Å
AuthorsManjula, R. / Murphy, E.L. / 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 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 8, 2021Group: Data collection / Database references / Category: citation / diffrn_detector
Item: _citation.journal_volume / _citation.title / _diffrn_detector.pdbx_collection_date
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)12,8043
Polymers12,6851
Non-polymers1192
Water1,36976
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)38,4119
Polymers38,0543
Non-polymers3576
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area7940 Å2
ΔGint-137 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.993, 73.993, 41.067
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-201-

SO4

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Components

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


Mass: 12684.659 Da / Num. of mol.: 1 / Mutation: P2G
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5 M Ammonium sulfate 0.1 M HEPES 7.5 30 % v/v (+/-)-2-Methyl-2,4-pentanediol

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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: May 14, 2021 / Details: Osmic VariMax ArcSec Cu-HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.51418 Å / Relative weight: 1
ReflectionResolution: 1.09→50 Å / Num. obs: 52539 / % possible obs: 98.2 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.012 / Rrim(I) all: 0.042 / Χ2: 0.896 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.09-1.126.40.38525950.9480.1560.4171.02273.2
1.12-1.147.30.36235670.9570.1390.3880.96399.9
1.14-1.177.70.32335500.9640.1210.3450.979100
1.17-1.218.10.29435400.9720.1080.3130.937100

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHENIX1.18_3845refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MSE

7mse


Resolution: 1.1→34.58 Å / SU ML: 0.0914 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6467
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.19 2501 4.99 %
Rwork0.1777 47645 -
obs0.1783 50146 95.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.82 Å2
Refinement stepCycle: LAST / Resolution: 1.1→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms881 0 6 76 963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069929
X-RAY DIFFRACTIONf_angle_d0.96241267
X-RAY DIFFRACTIONf_chiral_restr0.0795149
X-RAY DIFFRACTIONf_plane_restr0.0069164
X-RAY DIFFRACTIONf_dihedral_angle_d6.4707134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.120.2382710.23111476X-RAY DIFFRACTION53.07
1.12-1.140.2575730.21962090X-RAY DIFFRACTION73.62
1.14-1.160.2161210.21722459X-RAY DIFFRACTION90.53
1.16-1.190.22411480.2112747X-RAY DIFFRACTION98.1
1.19-1.220.23461300.21262729X-RAY DIFFRACTION99.79
1.22-1.250.24121330.19992801X-RAY DIFFRACTION99.9
1.25-1.290.17581460.20242741X-RAY DIFFRACTION100
1.29-1.330.21271380.20012784X-RAY DIFFRACTION100
1.33-1.380.25261620.20392764X-RAY DIFFRACTION100
1.38-1.440.21361670.20142763X-RAY DIFFRACTION99.97
1.44-1.50.19481580.19772723X-RAY DIFFRACTION100
1.5-1.580.20171500.17942795X-RAY DIFFRACTION100
1.58-1.680.15761490.18362762X-RAY DIFFRACTION99.9
1.68-1.810.20211370.17732794X-RAY DIFFRACTION99.86
1.81-1.990.19141570.18092767X-RAY DIFFRACTION99.86
1.99-2.280.19881470.17172804X-RAY DIFFRACTION99.93
2.28-2.870.16481340.17852811X-RAY DIFFRACTION99.97
2.87-34.580.18621800.16362835X-RAY DIFFRACTION99.77

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