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- PDB-4q3f: Human D-DT complexed with tartrate -

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Basic information

Entry
Database: PDB / ID: 4q3f
TitleHuman D-DT complexed with tartrate
ComponentsD-dopachrome decarboxylase
KeywordsLYASE / Tautomerase / cd74
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) / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / D-dopachrome decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRajasekaran, D. / Lolis, E.
CitationJournal: Faseb J. / Year: 2014
Title: Targeting distinct tautomerase sites of D-DT and MIF with a single molecule for inhibition of neutrophil lung recruitment.
Authors: Rajasekaran, D. / Zierow, S. / Syed, M. / Bucala, R. / Bhandari, V. / Lolis, E.J.
History
DepositionApr 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)38,2316
Polymers37,7813
Non-polymers4503
Water9,800544
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)38,2316
Polymers37,7813
Non-polymers4503
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 area7890 Å2
ΔGint-36 kcal/mol
Surface area13060 Å2
MethodPISA
2
B: D-dopachrome decarboxylase
hetero molecules

B: D-dopachrome decarboxylase
hetero molecules

B: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2316
Polymers37,7813
Non-polymers4503
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 area7900 Å2
ΔGint-33 kcal/mol
Surface area12760 Å2
MethodPISA
3
C: D-dopachrome decarboxylase
hetero molecules

C: D-dopachrome decarboxylase
hetero molecules

C: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2316
Polymers37,7813
Non-polymers4503
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area7980 Å2
ΔGint-33 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.730, 83.730, 40.560
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-387-

HOH

21A-392-

HOH

31A-433-

HOH

41A-437-

HOH

51A-488-

HOH

61B-397-

HOH

71B-408-

HOH

81B-416-

HOH

91C-356-

HOH

101C-399-

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: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.2 M Sodium tartrate dibasic dihydrate and 20% w/v Polyethylene glycol 3,350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 18, 2014
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→29.13 Å / Num. all: 74442 / Num. obs: 27672 / % possible obs: 93.8 %

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Processing

Software
NameVersionClassification
CrystalCleardata collection
REFMAC5.8.0069refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.13 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.517 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19827 1324 4.8 %RANDOM
Rwork0.14377 ---
obs0.14639 26344 93.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.236 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2655 0 30 544 3229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192733
X-RAY DIFFRACTIONr_bond_other_d0.0010.022676
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.9833705
X-RAY DIFFRACTIONr_angle_other_deg0.9073.0016150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.323.143105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69815450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7271521
X-RAY DIFFRACTIONr_chiral_restr0.1130.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213066
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
X-RAY DIFFRACTIONr_mcbond_it1.0471.1971401
X-RAY DIFFRACTIONr_mcbond_other1.0441.1961400
X-RAY DIFFRACTIONr_mcangle_it1.5081.7891746
X-RAY DIFFRACTIONr_mcangle_other1.5081.791747
X-RAY DIFFRACTIONr_scbond_it1.7151.3871332
X-RAY DIFFRACTIONr_scbond_other1.6981.3841329
X-RAY DIFFRACTIONr_scangle_other2.6122.0091958
X-RAY DIFFRACTIONr_long_range_B_refined5.37611.8513372
X-RAY DIFFRACTIONr_long_range_B_other5.37511.8393369
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 45 -
Rwork0.208 1234 -
obs--58 %

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