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- PDB-8dbb: Crystal structure of DDT with the selective inhibitor 2,5-Pyridin... -

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Basic information

Entry
Database: PDB / ID: 8dbb
TitleCrystal structure of DDT with the selective inhibitor 2,5-Pyridinedicarboxylic Acid
ComponentsD-dopachrome decarboxylase
KeywordsLYASE/INHIBITOR / Trimeric / Inhibitor / complex / enzyme / LYASE-INHIBITOR complex
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 / pyridine-2,5-dicarboxylic acid / D-dopachrome decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsParkins, A. / Banumathi, S. / Pantouris, G.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Structure / Year: 2023
Title: 2,5-Pyridinedicarboxylic acid is a bioactive and highly selective inhibitor of D-dopachrome tautomerase.
Authors: Parkins, A. / Das, P. / Prahaladan, V. / Rangel, V.M. / Xue, L. / Sankaran, B. / Bhandari, V. / Pantouris, G.
History
DepositionJun 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8687
Polymers38,1743
Non-polymers6934
Water9,098505
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint0 kcal/mol
Surface area18390 Å2
Unit cell
Length a, b, c (Å)83.721, 83.721, 40.633
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-462-

HOH

21A-466-

HOH

31A-470-

HOH

41B-468-

HOH

51B-471-

HOH

61C-449-

HOH

71C-451-

HOH

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Components

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


Mass: 12724.723 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: Chemical ChemComp-R3K / pyridine-2,5-dicarboxylic acid


Mass: 167.119 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H5NO4 / 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.: 505 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1 M sodium citrate, pH 5.20, 0.2 M ammonium acetate, 24-30% PEG4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.13→41.9 Å / Num. obs: 101870 / % possible obs: 85.4 % / Redundancy: 6.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.033 / Rrim(I) all: 0.082 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.13-1.152.70.352526219250.7940.2450.4313.232.5
6.19-41.865.10.12531866190.9690.0640.14124.684.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DPT

1dpt


Resolution: 1.3→41.9 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15663 3715 4.9 %RANDOM
Rwork0.12119 ---
obs0.1229 71400 95.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.603 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.3→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 49 505 3174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132739
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172619
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.6583725
X-RAY DIFFRACTIONr_angle_other_deg2.6961.5746019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.06221.382123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.70815429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2551519
X-RAY DIFFRACTIONr_chiral_restr0.1160.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023112
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02615
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_it0.830.7161405
X-RAY DIFFRACTIONr_mcbond_other0.8280.7161404
X-RAY DIFFRACTIONr_mcangle_it1.0251.0861752
X-RAY DIFFRACTIONr_mcangle_other1.0251.0861753
X-RAY DIFFRACTIONr_scbond_it1.7970.951334
X-RAY DIFFRACTIONr_scbond_other1.7350.9431332
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1321.351971
X-RAY DIFFRACTIONr_long_range_B_refined2.73111.1063020
X-RAY DIFFRACTIONr_long_range_B_other2.079.7212881
X-RAY DIFFRACTIONr_rigid_bond_restr11.91435358
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.175 274 -
Rwork0.137 5185 -
obs--93.65 %

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