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- PDB-8vfo: Crystal Structure of L117G Variant of D-Dopachrome Tautomerase (D-DT) -

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Basic information

Entry
Database: PDB / ID: 8vfo
TitleCrystal Structure of L117G 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
CITRIC ACID / D-dopachrome decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsParkins, A. / Pilien, 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 21, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7302
Polymers12,5371
Non-polymers1921
Water3,081171
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)38,1896
Polymers37,6123
Non-polymers5763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
Buried area7730 Å2
ΔGint-27 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.588, 80.588, 40.123
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 12537.421 Da / Num. of mol.: 1 / Mutation: L117G
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20-28% PEG 4000, 0.1M Sodium Citrate, 0.2M Ammonium Acetate
PH range: 5.8 - 6.2

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Data collection

DiffractionMean temperature: 90 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: Jun 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.35→40.29 Å / Num. obs: 21271 / % possible obs: 99.6 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.025 / Rrim(I) all: 0.056 / Net I/σ(I): 20.4 / Num. measured all: 96387
Reflection shellResolution: 1.35→1.37 Å / % possible obs: 94.8 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.252 / Num. measured all: 2853 / Num. unique obs: 1008 / CC1/2: 0.902 / Rpim(I) all: 0.171 / Rrim(I) all: 0.306 / Net I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→40.29 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1060 5 %RANDOM
Rwork0.166 ---
obs0.167 20211 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.35→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms856 0 13 171 1040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013884
X-RAY DIFFRACTIONr_bond_other_d0.0350.015853
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.6491201
X-RAY DIFFRACTIONr_angle_other_deg2.481.5771963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5575114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.75321.53839
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.13915141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.103156
X-RAY DIFFRACTIONr_chiral_restr0.0970.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02996
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02192
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_it0.8190.839459
X-RAY DIFFRACTIONr_mcbond_other0.7870.837458
X-RAY DIFFRACTIONr_mcangle_it1.2171.261572
X-RAY DIFFRACTIONr_mcangle_other1.2261.262573
X-RAY DIFFRACTIONr_scbond_it1.6910.994425
X-RAY DIFFRACTIONr_scbond_other1.6850.991423
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4421.432629
X-RAY DIFFRACTIONr_long_range_B_refined3.62712.322990
X-RAY DIFFRACTIONr_long_range_B_other3.27810.877933
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 90 -
Rwork0.21 1444 -
obs--95.4 %

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