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- PDB-3ker: D-Dopachrome tautomerase (D-DT)/ macrophage migration inhibitory ... -

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Basic information

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


D-dopachrome decarboxylase / D-dopachrome decarboxylase 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 / protease binding / positive regulation of ERK1 and ERK2 cascade ...D-dopachrome decarboxylase / D-dopachrome decarboxylase 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 / protease binding / positive regulation of ERK1 and ERK2 cascade / extracellular space / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.78 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 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 21, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,98224
Polymers51,8404
Non-polymers1,14220
Water1448
1
A: D-dopachrome decarboxylase
B: D-dopachrome decarboxylase
C: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,73718
Polymers38,8803
Non-polymers85715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2466
Polymers12,9601
Non-polymers2865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.172, 82.172, 144.253
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain A,A,A, using strict)
NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.2462, 0.2251, 0.9427), (0.8224, 0.5632, 0.0803), (-0.5129, 0.7951, -0.3238)4.4652, -21.5378, 46.777
3given(-0.2396, 0.8129, -0.5308), (0.2341, 0.579, 0.781), (0.9422, 0.0628, -0.329)42.4911, -25.6335, 12.2867
4given(-0.8261, 0.2096, 0.523), (-0.3698, 0.4986, -0.784), (-0.4251, -0.8411, -0.3344)47.2499, 5.4073, 42.1122

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Components

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


Mass: 12959.976 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ddt / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: O35215, D-dopachrome decarboxylase
#2: Chemical
ChemComp-RW1 / 4-phenylpyrimidine / 6-phenylpyrimidine


Mass: 156.184 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H8N2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1M Sodium Citrate, 0.1M Tris, 0.2M NaCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 15, 2009 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 13925 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.121 / Χ2: 0.732 / Net I/σ(I): 6.2
Reflection shellResolution: 2.78→2.88 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.514 / Num. unique all: 1384 / Χ2: 0.63 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.07 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.78 Å31.24 Å
Translation2.78 Å31.24 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KAN

3kan


Resolution: 2.78→31.23 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.809 / Cross valid method: THROUGHOUT / σ(F): 0
Details: One protein chain was refined using strict NCS, and NCS symmetry operators were used to generate the other three peptide polymers in the asymmetric unit. NCS averaged maps were also used. ...Details: One protein chain was refined using strict NCS, and NCS symmetry operators were used to generate the other three peptide polymers in the asymmetric unit. NCS averaged maps were also used. The deposited model therefore is an averaged model from all four peptide polymers in the asymmetric unit. The final model deposited has been generated by real-space transformations of chain A. The real space rotation matrix to generate chain B is described by: ( -0.24621 0.22510 0.94271 ) ( 0.82241 0.56320 0.08031 ) ( -0.51286 0.79507 -0.32379 ). The real space translation vector is described by: (4.46522 -21.53777 46.77695). Chain C was generated using real space rotation matrix: ( -0.23956 0.81293 -0.53080 ) ( 0.23408 0.57896 0.78104 ) ( 0.94224 0.06285 -0.32898 ) and real-space translation vector: (42.49111 -25.63348 12.28672). Chain D was generated using real space rotation matrix: ( -0.23956 0.81293 -0.53080 ) ( 0.23408 0.57896 0.78104 ) ( 0.94224 0.06285 -0.32898) and the real-space translation vector: (47.24985 5.40733 42.11218)
RfactorNum. reflection% reflectionSelection details
Rfree0.238 695 5 %random
Rwork0.222 ---
obs-13889 99.8 %-
Solvent computationBsol: 42.23 Å2
Displacement parametersBiso max: 79.24 Å2 / Biso mean: 42.715 Å2 / Biso min: 23.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.397 Å20 Å20 Å2
2---1.397 Å20 Å2
3---2.794 Å2
Refinement stepCycle: LAST / Resolution: 2.78→31.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3632 0 64 8 3704
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.39
X-RAY DIFFRACTIONc_mcbond_it1.1981.5
X-RAY DIFFRACTIONc_scbond_it2.1512
X-RAY DIFFRACTIONc_mcangle_it2.0722
X-RAY DIFFRACTIONc_scangle_it3.4732.5
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsTypeWeight
11AX-RAY DIFFRACTION0strict300
11AX-RAY DIFFRACTION0strict300
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5newDRGCNS.PARnewDRGCNS.TOP

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