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- PDB-3kan: D-dopachrome tautomerase (D-DT)/macrophage migration inhibitory f... -

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Basic information

Entry
Database: PDB / ID: 3kan
TitleD-dopachrome tautomerase (D-DT)/macrophage migration inhibitory factor 2 (MIF2) complexed with inhibitor 4-IPP
ComponentsD-dopachrome tautomerase
KeywordsCYTOKINE/INHIBITOR / Immune response / CYTOKINE / Tautomerase / CYTOKINE-INHIBITOR complex
Function / homology
Function and homology information


D-dopachrome decarboxylase / D-dopachrome decarboxylase activity / dopachrome isomerase activity / phenylpyruvate tautomerase activity / melanin biosynthetic process / 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 / phenylpyruvate tautomerase activity / melanin biosynthetic process / 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
4-phenylpyrimidine / D-dopachrome decarboxylase / D-dopachrome tautomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsZierow, S. / 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
DepositionOct 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 21, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-dopachrome tautomerase
B: D-dopachrome tautomerase
C: D-dopachrome tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3208
Polymers37,7813
Non-polymers5395
Water8,935496
1
A: D-dopachrome tautomerase
hetero molecules

A: D-dopachrome tautomerase
hetero molecules

A: D-dopachrome tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3559
Polymers37,7813
Non-polymers5756
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 area6710 Å2
ΔGint-35 kcal/mol
Surface area13310 Å2
MethodPISA
2
B: D-dopachrome tautomerase
hetero molecules

B: D-dopachrome tautomerase
hetero molecules

B: D-dopachrome tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3559
Polymers37,7813
Non-polymers5756
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 area6810 Å2
ΔGint-29 kcal/mol
Surface area13200 Å2
MethodPISA
3
C: D-dopachrome tautomerase
hetero molecules

C: D-dopachrome tautomerase
hetero molecules

C: D-dopachrome tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2496
Polymers37,7813
Non-polymers4693
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 area6860 Å2
ΔGint-31 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.286, 83.286, 40.303
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-193-

HOH

21B-174-

HOH

31B-291-

HOH

41C-164-

HOH

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Components

#1: Protein D-dopachrome tautomerase / D-dopachrome tautomerase / isoform CRA_b / cDNA FLJ76419 / highly similar to Homo sapiens D- ...D-dopachrome tautomerase / isoform CRA_b / cDNA FLJ76419 / highly similar to Homo sapiens D-dopachrome tautomerase (DDT) / mRNA


Mass: 12593.526 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: BL-21 / Gene: DDT, hCG_41098 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q53Y51, UniProt: P30046*PLUS
#2: Chemical ChemComp-RW1 / 4-phenylpyrimidine / 6-phenylpyrimidine


Mass: 156.184 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H8N2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Sodium chloride, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→50 Å / Num. all: 116532 / Num. obs: 116400 / % possible obs: 99.89 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 20.97
Reflection shellResolution: 1.13→1.17 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 4.31 / % possible all: 94.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DPT

1dpt


Resolution: 1.13→36.06 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.566 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12927 2329 2 %RANDOM
Rwork0.11172 ---
obs0.11208 114070 99.89 %-
all-114070 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.087 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.13→36.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2655 0 38 496 3189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222918
X-RAY DIFFRACTIONr_bond_other_d0.0010.022028
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9963988
X-RAY DIFFRACTIONr_angle_other_deg0.97434973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85223.504117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16915508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2091523
X-RAY DIFFRACTIONr_chiral_restr0.090.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213290
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
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_it1.2011.51836
X-RAY DIFFRACTIONr_mcbond_other0.3221.5743
X-RAY DIFFRACTIONr_mcangle_it1.88322981
X-RAY DIFFRACTIONr_scbond_it2.67231082
X-RAY DIFFRACTIONr_scangle_it3.9624.5982
X-RAY DIFFRACTIONr_rigid_bond_restr0.91434946
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.13→1.161 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.152 170 -
Rwork0.118 8425 -
obs--99.7 %

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