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- PDB-9bb0: D-Dopachrome Tautomerase with 4-Hydroxyphenylpyruvate Bound in Ca... -

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Basic information

Entry
Database: PDB / ID: 9bb0
TitleD-Dopachrome Tautomerase with 4-Hydroxyphenylpyruvate Bound in Catalytic Site at Atomic (0.98 Angstrom) Resolution
ComponentsD-dopachrome decarboxylase
KeywordsCYTOKINE / tautomerase / keto-enol tautomerase / substrate / 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
Chem-EN1 / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / D-dopachrome decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.985 Å
AuthorsParkins, A. / Argueta, C. / Pantouris, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published / Year: 2025
Title: D-Dopachrome Tautomerase with 4-Hydroxyphenylpyruvate Bound in Catalytic Site at Atomic (0.98 Angstrom) Resolution
Authors: Argueta, C. / Parkins, A. / Pantouris, G.
History
DepositionApr 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: 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

Downloads & links

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Assembly

Deposited unit
AAA: D-dopachrome decarboxylase
BBB: D-dopachrome decarboxylase
CCC: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,30212
Polymers37,7813
Non-polymers5219
Water8,755486
1
AAA: D-dopachrome decarboxylase
hetero molecules

AAA: D-dopachrome decarboxylase
hetero molecules

AAA: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9199
Polymers37,7813
Non-polymers1386
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 area7470 Å2
ΔGint-97 kcal/mol
Surface area13120 Å2
MethodPISA
2
BBB: D-dopachrome decarboxylase
hetero molecules

BBB: D-dopachrome decarboxylase
hetero molecules

BBB: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,06818
Polymers37,7813
Non-polymers1,28815
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 area9000 Å2
ΔGint-120 kcal/mol
Surface area12900 Å2
MethodPISA
3
CCC: D-dopachrome decarboxylase
hetero molecules

CCC: D-dopachrome decarboxylase
hetero molecules

CCC: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9199
Polymers37,7813
Non-polymers1386
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 area7600 Å2
ΔGint-98 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.765, 83.765, 40.535
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11AAA-468-

HOH

21AAA-470-

HOH

31BBB-460-

HOH

41BBB-462-

HOH

51CCC-443-

HOH

61CCC-446-

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 BL21 (bacteria) / References: UniProt: P30046, D-dopachrome decarboxylase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: Na
#3: Chemical ChemComp-ENO / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / HPP


Mass: 180.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EN1 / (2E)-2-hydroxy-3-(4-hydroxyphenyl)prop-2-enoic acid


Mass: 180.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H8O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 43.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.2M Ammonium Acetate, 0.1M Sodium Citrate pH 5.9, 28% PEG 4000 - soaked into 0.2M Ammonium Acetate, 0.1M Sodium Citrate pH 5.9, 33% PEG 4000, 600mM 4-Hydroxyphenylpyruvate

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 0.98→72.54 Å / Num. obs: 178449 / % possible obs: 99.1 % / Redundancy: 9.5 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.013 / Rrim(I) all: 0.042 / Χ2: 0.93 / Net I/σ(I): 23.1 / Num. measured all: 1686804
Reflection shellResolution: 0.98→1 Å / % possible obs: 84.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 1.24 / Num. measured all: 40904 / Num. unique obs: 7549 / CC1/2: 0.548 / Rpim(I) all: 0.554 / Rrim(I) all: 1.368 / Χ2: 0.55 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.985→72.54 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / Cross valid method: THROUGHOUT / ESU R: 0.004 / ESU R Free: 0.004
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1467 8881 4.98 %
Rwork0.1321 169470 -
all0.133 --
obs-178351 99.086 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.706 Å2
Baniso -1Baniso -2Baniso -3
1-0.014 Å20 Å20 Å2
2--0.014 Å20 Å2
3----0.029 Å2
Refinement stepCycle: LAST / Resolution: 0.985→72.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 33 496 3164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132936
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172795
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.654025
X-RAY DIFFRACTIONr_angle_other_deg2.6221.5716467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.19221.908131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53915466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5911519
X-RAY DIFFRACTIONr_chiral_restr0.1150.2392
X-RAY DIFFRACTIONr_chiral_restr_other2.7840.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023454
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02658
X-RAY DIFFRACTIONr_nbd_refined0.2390.2613
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.22316
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21415
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2254
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.226
X-RAY DIFFRACTIONr_nbd_other0.280.2177
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3570.269
X-RAY DIFFRACTIONr_mcbond_it10.7371.1021528
X-RAY DIFFRACTIONr_mcbond_other10.7441.1011526
X-RAY DIFFRACTIONr_mcangle_it10.8671.5851945
X-RAY DIFFRACTIONr_mcangle_other10.8651.5851946
X-RAY DIFFRACTIONr_scbond_it19.3131.5091408
X-RAY DIFFRACTIONr_scbond_other19.3061.5091409
X-RAY DIFFRACTIONr_scangle_it13.3782.0772080
X-RAY DIFFRACTIONr_scangle_other13.3752.0762081
X-RAY DIFFRACTIONr_lrange_it10.21615.2333324
X-RAY DIFFRACTIONr_lrange_other10.18714.1623189
X-RAY DIFFRACTIONr_rigid_bond_restr39.72435731
X-RAY DIFFRACTIONr_ncsr_local_group_10.0760.053713
X-RAY DIFFRACTIONr_ncsr_local_group_20.0850.053649
X-RAY DIFFRACTIONr_ncsr_local_group_30.0990.053648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.985-1.0110.19262311120X-RAY DIFFRACTION88.0813
1.011-1.0380.1376300.12812299X-RAY DIFFRACTION99.6378
1.038-1.0680.1156690.10912012X-RAY DIFFRACTION100
1.068-1.1010.1075870.10511605X-RAY DIFFRACTION100
1.101-1.1370.1196490.10811212X-RAY DIFFRACTION100
1.137-1.1770.1236100.11810920X-RAY DIFFRACTION100
1.177-1.2220.1315860.11510478X-RAY DIFFRACTION100
1.222-1.2710.1355470.11710141X-RAY DIFFRACTION100
1.271-1.3280.1314470.1159801X-RAY DIFFRACTION99.9902
1.328-1.3930.1454680.1259312X-RAY DIFFRACTION100
1.393-1.4680.1434400.1318813X-RAY DIFFRACTION100
1.468-1.5570.1474360.1318398X-RAY DIFFRACTION99.9774
1.557-1.6650.1544220.1327848X-RAY DIFFRACTION100
1.665-1.7980.1553300.1357341X-RAY DIFFRACTION100
1.798-1.9690.153150.1326757X-RAY DIFFRACTION100
1.969-2.2020.1473460.1286085X-RAY DIFFRACTION99.9534
2.202-2.5420.1622450.1355385X-RAY DIFFRACTION100
2.542-3.1120.1742660.1484502X-RAY DIFFRACTION100
3.112-4.3970.1311660.133511X-RAY DIFFRACTION99.9456
4.397-72.50.194990.1861930X-RAY DIFFRACTION99.9507

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