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- PDB-1dpt: D-DOPACHROME TAUTOMERASE -

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Basic information

Entry
Database: PDB / ID: 1dpt
TitleD-DOPACHROME TAUTOMERASE
ComponentsD-DOPACHROME TAUTOMERASE
KeywordsCYTOKINE / GROWTH FACTOR / TAUTOMERASE
Function / homology
Function and homology information


D-dopachrome decarboxylase / D-dopachrome decarboxylase activity / melanin biosynthetic process / dopachrome isomerase activity / 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 / melanin biosynthetic process / dopachrome isomerase activity / 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
D-dopachrome decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsSugimoto, 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
DepositionMay 11, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 6, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_distant_solvent_atoms ...pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)37,7813
Polymers37,7813
Non-polymers00
Water4,468248
1
A: D-DOPACHROME TAUTOMERASE


Theoretical massNumber of molelcules
Total (without water)12,5941
Polymers12,5941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-DOPACHROME TAUTOMERASE


Theoretical massNumber of molelcules
Total (without water)12,5941
Polymers12,5941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: D-DOPACHROME TAUTOMERASE


Theoretical massNumber of molelcules
Total (without water)12,5941
Polymers12,5941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.230, 84.230, 40.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.38826, -0.92154, -0.00293), (-0.92155, -0.38826, -0.00092), (-0.00029, 0.00306, -1)42.28216, 24.39487, 71.35732
2given(-0.56869, 0.82255, 0.00292), (-0.82255, -0.56869, -0.00011), (0.00157, -0.00246, 1)-0.12202, 48.66496, -1.05978

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Components

#1: Protein D-DOPACHROME TAUTOMERASE


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 / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.21 Å3/Da / Density % sol: 45 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD.
Crystal growpH: 5.7 / Details: pH 5.7
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2100 mMTris-HCl1drop
323 %(w/v)PEG40001reservoir
40.1 Msodium citrate1reservoir
50.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
CCP4data scaling
X-PLOR3.851phasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1759 4 %RANDOM
Rwork0.164 ---
obs0.164 43723 90.9 %-
Displacement parametersBiso mean: 14.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.54→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2655 0 0 248 2903
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.82
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.081.5
X-RAY DIFFRACTIONx_mcangle_it1.62
X-RAY DIFFRACTIONx_scbond_it2.752
X-RAY DIFFRACTIONx_scangle_it4.532.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.54→1.61 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.31 205 4.2 %
Rwork0.275 4713 -
obs--81.7 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor obs: 0.275

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