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- PDB-8vdy: Crystal Structure of Delta 114-117 D-Dopachrome Tautomerase (D-DT) -

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Basic information

Entry
Database: PDB / ID: 8vdy
TitleCrystal Structure of Delta 114-117 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
D-dopachrome decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 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 18, 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_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
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
D: D-dopachrome decarboxylase
E: D-dopachrome decarboxylase
F: D-dopachrome decarboxylase
G: D-dopachrome decarboxylase
H: D-dopachrome decarboxylase
I: D-dopachrome decarboxylase
J: D-dopachrome decarboxylase
K: D-dopachrome decarboxylase
L: D-dopachrome decarboxylase


Theoretical massNumber of molelcules
Total (without water)145,21112
Polymers145,21112
Non-polymers00
Water1267
1
A: D-dopachrome decarboxylase
B: D-dopachrome decarboxylase
C: D-dopachrome decarboxylase


Theoretical massNumber of molelcules
Total (without water)36,3033
Polymers36,3033
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-24 kcal/mol
Surface area12280 Å2
MethodPISA
2
D: D-dopachrome decarboxylase
E: D-dopachrome decarboxylase

F: D-dopachrome decarboxylase


Theoretical massNumber of molelcules
Total (without water)36,3033
Polymers36,3033
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area6220 Å2
ΔGint-21 kcal/mol
Surface area12380 Å2
MethodPISA
3
G: D-dopachrome decarboxylase

K: D-dopachrome decarboxylase

L: D-dopachrome decarboxylase


Theoretical massNumber of molelcules
Total (without water)36,3033
Polymers36,3033
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area6040 Å2
ΔGint-24 kcal/mol
Surface area12360 Å2
MethodPISA
4
H: D-dopachrome decarboxylase
I: D-dopachrome decarboxylase
J: D-dopachrome decarboxylase


Theoretical massNumber of molelcules
Total (without water)36,3033
Polymers36,3033
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-24 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.533, 59.529, 129.976
Angle α, β, γ (deg.)90.00, 107.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 12100.895 Da / Num. of mol.: 12 / Mutation: Delta 114-117
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 26-32% PEG 3350, 0.25-0.275M Ammonium Acetate.

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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: Apr 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.44→89.84 Å / Num. obs: 51582 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.953 / Rmerge(I) obs: 0.267 / Net I/σ(I): 4.5
Reflection shellResolution: 2.44→2.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.363 / Mean I/σ(I) obs: 1 / Num. unique obs: 51582 / CC1/2: 0.25 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→89.84 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.836 / Cross valid method: THROUGHOUT / ESU R: 0.506 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30177 2702 5 %RANDOM
Rwork0.24878 ---
obs0.25138 51582 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.01 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.44→89.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9380 0 0 7 9387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139573
X-RAY DIFFRACTIONr_bond_other_d0.0360.0159065
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.63313000
X-RAY DIFFRACTIONr_angle_other_deg2.5411.56620786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02551271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26820.979439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.944151429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0151572
X-RAY DIFFRACTIONr_chiral_restr0.0660.21286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210964
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022188
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_it2.0412.915117
X-RAY DIFFRACTIONr_mcbond_other2.0412.915117
X-RAY DIFFRACTIONr_mcangle_it3.2374.3576368
X-RAY DIFFRACTIONr_mcangle_other3.2374.3576369
X-RAY DIFFRACTIONr_scbond_it1.8363.0444456
X-RAY DIFFRACTIONr_scbond_other1.8363.0444457
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9654.56632
X-RAY DIFFRACTIONr_long_range_B_refined4.86134.6369599
X-RAY DIFFRACTIONr_long_range_B_other4.8634.6379599
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 223 -
Rwork0.341 3750 -
obs--98.68 %

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