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- PDB-8vfk: Crystal Structure of Delta 109-117 D-Dopachrome Tautomerase (D-DT) -

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Basic information

Entry
Database: PDB / ID: 8vfk
TitleCrystal Structure of Delta 109-117 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
CITRATE ANION / D-dopachrome decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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 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 15, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.method_details
Revision 1.3May 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
B: D-dopachrome decarboxylase
C: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2056
Polymers34,8043
Non-polymers4013
Water3,819212
1
A: D-dopachrome decarboxylase
B: D-dopachrome decarboxylase
hetero molecules

C: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2056
Polymers34,8043
Non-polymers4013
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_564y,-x+y+1,z-1/61
Buried area5950 Å2
ΔGint-30 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.496, 75.496, 96.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 11601.270 Da / Num. of mol.: 3 / Mutation: Delta 109-117
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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 26-28% PEG 4000, 0.1M Sodium Citrate pH 6.0-6.2, 0.2M Ammonium Acetate
PH range: 6.0-6.2

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Data collection

DiffractionMean temperature: 290 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 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.59→65.38 Å / Num. obs: 41389 / % possible obs: 98.5 % / Redundancy: 11.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.247 / Rpim(I) all: 0.075 / Rrim(I) all: 0.258 / Net I/σ(I): 4.9 / Num. measured all: 479440
Reflection shellResolution: 1.59→1.62 Å / % possible obs: 97.2 % / Redundancy: 11.8 % / Rmerge(I) obs: 1.875 / Num. measured all: 24220 / Num. unique obs: 2046 / CC1/2: 0.469 / Rpim(I) all: 0.56 / Rrim(I) all: 1.957 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→65.38 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18472 2065 5 %RANDOM
Rwork0.17616 ---
obs0.1766 39321 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.454 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.59→65.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 27 212 2581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132452
X-RAY DIFFRACTIONr_bond_other_d0.0350.0152340
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.6343341
X-RAY DIFFRACTIONr_angle_other_deg2.3961.5645389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6795325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85421.161112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01315379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0311518
X-RAY DIFFRACTIONr_chiral_restr0.090.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022791
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02549
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_it1.9191.8291275
X-RAY DIFFRACTIONr_mcbond_other1.921.8291271
X-RAY DIFFRACTIONr_mcangle_it32.7361590
X-RAY DIFFRACTIONr_mcangle_other32.7351589
X-RAY DIFFRACTIONr_scbond_it2.9072.1641177
X-RAY DIFFRACTIONr_scbond_other2.9082.161176
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6433.1141744
X-RAY DIFFRACTIONr_long_range_B_refined6.30523.8922563
X-RAY DIFFRACTIONr_long_range_B_other6.21323.5552535
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 171 -
Rwork0.308 2851 -
obs--97.2 %

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