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- PDB-8vg5: Crystal Structure of V113N Variant of D-Dopachrome Tautomerase (D... -

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Basic information

Entry
Database: PDB / ID: 8vg5
TitleCrystal Structure of V113N Variant of D-Dopachrome Tautomerase (D-DT) Bound with 4CPPC
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
4-(3-carboxyphenyl)pyridine-2,5-dicarboxylic acid / CITRIC ACID / D-dopachrome decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 22, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,9136
Polymers50,4344
Non-polymers4792
Water9,710539
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)38,6876
Polymers37,8253
Non-polymers8623
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5840 Å2
ΔGint-31 kcal/mol
Surface area13220 Å2
MethodPISA
2
B: D-dopachrome decarboxylase
C: D-dopachrome decarboxylase
D: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0184
Polymers37,8253
Non-polymers1921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-28 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.093, 111.093, 66.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-370-

HOH

21A-420-

HOH

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Components

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


Mass: 12608.498 Da / Num. of mol.: 4 / Mutation: V113N
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-7L9 / 4-(3-carboxyphenyl)pyridine-2,5-dicarboxylic acid


Mass: 287.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9NO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 26-32% PEG 4000, 0.1M Sodium Citrate, 0.2M Ammonium Acetate
PH range: 5.2-6.8

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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: Apr 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.5→55.6 Å / Num. obs: 73626 / % possible obs: 99.1 % / Redundancy: 17 % / CC1/2: 0.992 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.056 / Rrim(I) all: 0.239 / Net I/σ(I): 6.5
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 95.2 % / Redundancy: 9.1 % / Rmerge(I) obs: 1.974 / Num. measured all: 31856 / Num. unique obs: 3502 / CC1/2: 0.481 / Rpim(I) all: 0.679 / Rrim(I) all: 2.093 / Net I/σ(I) obs: 0.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→55.6 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26196 3613 4.9 %RANDOM
Rwork0.22674 ---
obs0.22845 69924 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.384 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.5→55.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 34 558 3896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133403
X-RAY DIFFRACTIONr_bond_other_d0.0350.0153269
X-RAY DIFFRACTIONr_angle_refined_deg1.451.6424621
X-RAY DIFFRACTIONr_angle_other_deg2.4391.577518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4745441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84121.667150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2615534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2151522
X-RAY DIFFRACTIONr_chiral_restr0.0710.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023853
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02754
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_it1.8892.5371775
X-RAY DIFFRACTIONr_mcbond_other1.8862.5351773
X-RAY DIFFRACTIONr_mcangle_it2.7983.7982211
X-RAY DIFFRACTIONr_mcangle_other2.7963.7982211
X-RAY DIFFRACTIONr_scbond_it2.4132.741628
X-RAY DIFFRACTIONr_scbond_other2.4122.7411629
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7534.0262411
X-RAY DIFFRACTIONr_long_range_B_refined6.04332.883917
X-RAY DIFFRACTIONr_long_range_B_other5.8131.9923750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 225 -
Rwork0.388 4957 -
obs--94.8 %

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