+Open data
-Basic information
Entry | Database: PDB / ID: 1dpt | ||||||
---|---|---|---|---|---|---|---|
Title | D-DOPACHROME TAUTOMERASE | ||||||
Components | D-DOPACHROME TAUTOMERASE | ||||||
Keywords | CYTOKINE / GROWTH FACTOR / TAUTOMERASE | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Sugimoto, H. / Taniguchi, M. / Nakagawa, A. / Tanaka, I. | ||||||
Citation | Journal: Biochemistry / Year: 1999 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: Journal: Biochem.Biophys.Res.Commun. / Year: 1998 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: Journal: J.Struct.Biol. / Year: 1997 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dpt.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dpt.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 1dpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dpt_validation.pdf.gz | 420.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1dpt_full_validation.pdf.gz | 420.1 KB | Display | |
Data in XML | 1dpt_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 1dpt_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/1dpt ftp://data.pdbj.org/pub/pdb/validation_reports/dp/1dpt | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 12593.526 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Organ: LIVER / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) LYSS / References: UniProt: P30046 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 45 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD. | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 283 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 |
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 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.275 |