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- PDB-8vg7: Crystal Structure of T115A Variant of D-Dopachrome Tautomerase (D-DT) -

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Basic information

Entry
Database: PDB / ID: 8vg7
TitleCrystal Structure of T115A Variant of D-Dopachrome Tautomerase (D-DT)
ComponentsD-dopachrome decarboxylase
KeywordsISOMERASE / Truncation / Enzyme / Cytokine
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsParkins, A. / Pilien, A. / Wolff, A. / Thompson, M.C. / Pantouris, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: The C-terminal Region of D-DT Regulates Molecular Recognition for Protein-Ligand Complexes.
Authors: Parkins, A. / Pilien, A.V.R. / Wolff, A.M. / Argueta, C. / Vargas, J. / Sadeghi, S. / Franz, A.H. / Thompson, M.C. / Pantouris, G.
History
DepositionDec 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-dopachrome decarboxylase


Theoretical massNumber of molelcules
Total (without water)12,5641
Polymers12,5641
Non-polymers00
Water1,78399
1
A: D-dopachrome decarboxylase

A: D-dopachrome decarboxylase

A: D-dopachrome decarboxylase


Theoretical massNumber of molelcules
Total (without water)37,6913
Polymers37,6913
Non-polymers00
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 area6840 Å2
ΔGint-35 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.281, 82.281, 40.732
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-298-

HOH

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Components

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


Mass: 12563.500 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 28-30% PEG 4000, 0.1M Sodium Citrate pH 5.8-6.2, 0.2M Ammonium Acetate
PH range: 5.8 - 6.2

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Data collection

DiffractionMean temperature: 280 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.24→41.14 Å / Num. obs: 29080 / % possible obs: 99.8 % / Redundancy: 4.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.035 / Rrim(I) all: 0.079 / Net I/σ(I): 14.2 / Num. measured all: 137298
Reflection shellResolution: 1.24→1.26 Å / % possible obs: 96.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.269 / Num. measured all: 3585 / Num. unique obs: 1387 / CC1/2: 0.875 / Rpim(I) all: 0.195 / Rrim(I) all: 0.334 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→41.14 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.763 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12343 1443 5 %RANDOM
Rwork0.09977 ---
obs0.10091 27635 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.128 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.24→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 0 99 982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.013900
X-RAY DIFFRACTIONr_bond_other_d0.0010.015884
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.6371220
X-RAY DIFFRACTIONr_angle_other_deg1.5961.5682032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9295116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.520.95242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11815149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.181157
X-RAY DIFFRACTIONr_chiral_restr0.1380.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021018
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02204
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0930.979467
X-RAY DIFFRACTIONr_mcbond_other1.0930.976466
X-RAY DIFFRACTIONr_mcangle_it1.3741.485582
X-RAY DIFFRACTIONr_mcangle_other1.3731.487583
X-RAY DIFFRACTIONr_scbond_it2.8881.41433
X-RAY DIFFRACTIONr_scbond_other2.8881.41433
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5631.942638
X-RAY DIFFRACTIONr_long_range_B_refined3.18713.539933
X-RAY DIFFRACTIONr_long_range_B_other3.04312.979921
X-RAY DIFFRACTIONr_rigid_bond_restr5.31331784
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.24→1.272 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.119 87 -
Rwork0.1 2018 -
obs--96.87 %

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