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- PDB-6c5f: Human D-Dopachrome tautomerase (D-DT)/ macrophage migration inhib... -

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Basic information

Entry
Database: PDB / ID: 6c5f
TitleHuman D-Dopachrome tautomerase (D-DT)/ macrophage migration inhibitory factor 2 (MIF2) complexed with the selective inhibitor 4-CPPC
ComponentsD-dopachrome decarboxylase
KeywordsCYTOKINE / selective inhibitor
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
4-(3-carboxyphenyl)pyridine-2,5-dicarboxylic acid / D-dopachrome decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsPantouris, G. / Lolis, E.J.
CitationJournal: Biochemistry / Year: 2018
Title: Structural Plasticity in the C-Terminal Region of Macrophage Migration Inhibitory Factor-2 Is Associated with an Induced Fit Mechanism for a Selective Inhibitor.
Authors: Pantouris, G. / Bucala, R. / Lolis, E.J.
History
DepositionJan 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)38,0684
Polymers37,7813
Non-polymers2871
Water7,206400
1
A: D-dopachrome decarboxylase

A: D-dopachrome decarboxylase

A: D-dopachrome decarboxylase


Theoretical massNumber of molelcules
Total (without water)37,7813
Polymers37,7813
Non-polymers00
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 area6600 Å2
ΔGint-32 kcal/mol
Surface area13140 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)38,6426
Polymers37,7813
Non-polymers8623
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area6290 Å2
ΔGint-34 kcal/mol
Surface area12700 Å2
MethodPISA
3
C: D-dopachrome decarboxylase

C: D-dopachrome decarboxylase

C: D-dopachrome decarboxylase


Theoretical massNumber of molelcules
Total (without water)37,7813
Polymers37,7813
Non-polymers00
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 area6550 Å2
ΔGint-33 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.936, 83.936, 40.479
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA1 - 1121 - 112
21THRTHRBB1 - 1121 - 112
12LEULEUAA1 - 1171 - 117
22LEULEUCC1 - 1171 - 117
13THRTHRBB1 - 1121 - 112
23THRTHRCC1 - 1121 - 112

NCS ensembles :
ID
1
2
3

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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-7L9 / 4-(3-carboxyphenyl)pyridine-2,5-dicarboxylic acid


Mass: 287.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 28% - 34% PEG 4000, 0.1 M sodium citrate tribasic dihydrate, pH 5.8, 0.2 M Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 63056 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.013 / Rrim(I) all: 0.042 / Χ2: 2.697 / Net I/σ(I): 33.8
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.4-1.425.20.14731680.9830.0710.1641.518
1.42-1.455.40.14231710.3870.070.1591.796
1.45-1.485.60.12131310.9890.0560.1331.774
1.48-1.515.80.11131210.9910.050.1221.739
1.51-1.5460.10131510.9930.0450.111.984
1.54-1.586.20.08131810.9950.0350.0891.695
1.58-1.626.40.07631520.9960.0330.0831.812
1.62-1.666.60.0731350.9970.0290.0761.905
1.66-1.716.90.06631490.9970.0270.0711.998
1.71-1.767.20.0631770.9980.0240.0652.052
1.76-1.837.50.05531570.9980.0220.0592.164
1.83-1.97.80.05331300.9980.020.0562.612
1.9-1.998.20.04731600.9990.0180.052.655
1.99-2.098.60.04731480.9990.0170.053.086
2.09-2.2290.04131610.9990.0140.0432.922
2.22-2.399.40.04131550.9990.0140.0443.184
2.39-2.63100.03531320.9990.0120.0372.782
2.63-3.0210.40.03431730.9990.0110.0352.988
3.02-3.810.40.03531400.9990.0110.0374.049
3.8-5014.60.03831640.9990.010.0394.395

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
MOLREPphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DPT

1dpt


Resolution: 1.4→41.97 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.431 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1567 3045 4.8 %RANDOM
Rwork0.1177 ---
obs0.1195 60002 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.38 Å2 / Biso mean: 15.075 Å2 / Biso min: 6.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.4→41.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2572 0 21 404 2997
Biso mean--16.83 29.74 -
Num. residues----347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0192667
X-RAY DIFFRACTIONr_bond_other_d0.0020.022524
X-RAY DIFFRACTIONr_angle_refined_deg2.011.9823628
X-RAY DIFFRACTIONr_angle_other_deg1.9613.0015836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6925350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26223.43499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.53215424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3181518
X-RAY DIFFRACTIONr_chiral_restr0.1510.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212988
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02537
X-RAY DIFFRACTIONr_rigid_bond_restr5.47235191
X-RAY DIFFRACTIONr_sphericity_free25.3925267
X-RAY DIFFRACTIONr_sphericity_bonded9.75155275
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A65340.07
12B65340.07
21A70020.07
22C70020.07
31B65700.08
32C65700.08
LS refinement shellResolution: 1.398→1.434 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 228 -
Rwork0.107 4391 -
all-4619 -
obs--98.57 %

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