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Open data
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Basic information
Entry | Database: PDB / ID: 1dpt | ||||||
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Title | D-DOPACHROME TAUTOMERASE | ||||||
![]() | D-DOPACHROME TAUTOMERASE | ||||||
![]() | CYTOKINE / GROWTH FACTOR / TAUTOMERASE | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugimoto, H. / Taniguchi, M. / Nakagawa, A. / Tanaka, I. | ||||||
![]() | ![]() Title: Crystal structure of human D-dopachrome tautomerase, a homologue of macrophage migration inhibitory factor, at 1.54 A resolution. Authors: Sugimoto, H. / Taniguchi, M. / Nakagawa, A. / Tanaka, I. / Suzuki, M. / Nishihira, J. #1: ![]() Title: Molecular Cloning of Human D-Dopachrome Tautomerase Cdna: N-Terminal Proline is Essential for Enzyme Activation Authors: Nishihira, J. / Fujinaga, M. / Kuriyama, T. / Suzuki, M. / Sugimoto, H. / Nakagawa, A. / Tanaka, I. / Sakai, M. #2: ![]() Title: Crystallization and Preliminary X-Ray Analysis of Human D-Dopachrome Tautomerase Authors: Sugimoto, H. / Taniguchi, M. / Nakagawa, A. / Tanaka, I. / Suzuki, M. / Nishihira, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.3 KB | Display | ![]() |
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PDB format | ![]() | 61.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.1 KB | Display | ![]() |
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Full document | ![]() | 420.1 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 12593.526 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 45 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD. | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.7 / Details: pH 5.7 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→20 Å / Num. obs: 43724 / % possible obs: 90.9 % / Observed criterion σ(I): 6 / Redundancy: 2.4 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.54→1.62 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.4 / % possible all: 81.9 |
Reflection | *PLUS Num. measured all: 104959 |
Reflection shell | *PLUS % possible obs: 81.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: HUMAN MACROPHAGE MIGRATION INHIBITORY FACTOR Resolution: 1.54→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 14.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.54→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.54→1.61 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.275 |