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- PDB-8vfl: Crystal Structure of WT D-Dopachrome Tautomerase (D-DT) at 290K -

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Basic information

Entry
Database: PDB / ID: 8vfl
TitleCrystal Structure of WT D-Dopachrome Tautomerase (D-DT) at 290K
ComponentsD-dopachrome decarboxylase
KeywordsISOMERASE / Truncation / Enzyme / Cytokine
Function / homology
Function and homology information


D-dopachrome decarboxylase / D-dopachrome decarboxylase activity / melanin biosynthetic process / dopachrome isomerase activity / 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 / melanin biosynthetic process / dopachrome isomerase activity / 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: 1.23 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_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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


Theoretical massNumber of molelcules
Total (without water)37,7813
Polymers37,7813
Non-polymers00
Water5,332296
1
A: D-dopachrome decarboxylase

A: D-dopachrome decarboxylase

A: D-dopachrome decarboxylase


Theoretical massNumber of molelcules
Total (without water)37,7813
Polymers37,7813
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 area6750 Å2
ΔGint-33 kcal/mol
Surface area13470 Å2
MethodPISA
2
B: D-dopachrome decarboxylase

B: D-dopachrome decarboxylase

B: D-dopachrome decarboxylase


Theoretical massNumber of molelcules
Total (without water)37,7813
Polymers37,7813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6700 Å2
ΔGint-35 kcal/mol
Surface area13420 Å2
MethodPISA
3
C: D-dopachrome decarboxylase

C: D-dopachrome decarboxylase

C: D-dopachrome decarboxylase


Theoretical massNumber of molelcules
Total (without water)37,7813
Polymers37,7813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6790 Å2
ΔGint-35 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.351, 84.351, 41.032
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-400-

HOH

21B-302-

HOH

31C-292-

HOH

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Components

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


Mass: 12593.526 Da / Num. of mol.: 3
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 / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 24-30% PEG 4000, 0.1M Sodium Citrate (pH 5.6-6.0), 0.2M Ammonium Acetate
PH range: 5.6 - 6.0

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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: 1.23→73.05 Å / Num. obs: 87432 / % possible obs: 92.1 % / Redundancy: 4.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.044 / Rrim(I) all: 0.097 / Net I/σ(I): 8.1 / Num. measured all: 377938
Reflection shellResolution: 1.23→1.25 Å / % possible obs: 44 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.879 / Num. measured all: 3791 / Num. unique obs: 2118 / CC1/2: 0.268 / Rpim(I) all: 0.812 / Rrim(I) all: 1.201 / Net I/σ(I) obs: 0.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→73.05 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17988 4224 4.8 %RANDOM
Rwork0.14325 ---
obs0.14503 83207 92.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.23→73.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 0 296 2948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132725
X-RAY DIFFRACTIONr_bond_other_d0.0350.0152663
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.6383700
X-RAY DIFFRACTIONr_angle_other_deg2.691.5666136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9755356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.16621.024127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49315452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5211521
X-RAY DIFFRACTIONr_chiral_restr0.1150.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023086
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02616
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_it1.441.2121409
X-RAY DIFFRACTIONr_mcbond_other1.4351.2111408
X-RAY DIFFRACTIONr_mcangle_it1.7121.8291758
X-RAY DIFFRACTIONr_mcangle_other1.7141.831759
X-RAY DIFFRACTIONr_scbond_it2.9381.631316
X-RAY DIFFRACTIONr_scbond_other2.9371.6291316
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.372.2811937
X-RAY DIFFRACTIONr_long_range_B_refined3.27916.3532866
X-RAY DIFFRACTIONr_long_range_B_other3.07715.8292824
X-RAY DIFFRACTIONr_rigid_bond_restr12.02835388
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 204 -
Rwork0.394 3113 -
obs--47.02 %

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