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- PDB-7mse: High-resolution crystal structure of hMIF2 with tartrate at the a... -

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Basic information

Entry
Database: PDB / ID: 7mse
TitleHigh-resolution crystal structure of hMIF2 with tartrate at the active site
ComponentsD-dopachrome decarboxylase
KeywordsCYTOKINE
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) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
L(+)-TARTARIC ACID / D-dopachrome decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.27 Å
AuthorsMurphy, E.L. / Manjula, R. / Murphy, J.W. / Lolis, E.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase.
Authors: Chen, E. / Reiss, K. / Shah, D. / Manjula, R. / Allen, B. / Murphy, E.L. / Murphy, J.W. / Batista, V.S. / Bhandari, V. / Lolis, E.J. / Lisi, G.P.
History
DepositionMay 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 8, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)38,2316
Polymers37,7813
Non-polymers4503
Water7,278404
1
A: D-dopachrome decarboxylase
hetero molecules

A: D-dopachrome decarboxylase
hetero molecules

A: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2316
Polymers37,7813
Non-polymers4503
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7680 Å2
ΔGint-34 kcal/mol
Surface area12860 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)38,2316
Polymers37,7813
Non-polymers4503
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 area7690 Å2
ΔGint-38 kcal/mol
Surface area12960 Å2
MethodPISA
3
C: D-dopachrome decarboxylase
hetero molecules

C: D-dopachrome decarboxylase
hetero molecules

C: D-dopachrome decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2316
Polymers37,7813
Non-polymers4503
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7990 Å2
ΔGint-32 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.396, 83.396, 40.429
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3

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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-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 28.6% w/v PEG 3350, 0.31M sodium tartrate at pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.51418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.51418 Å / Relative weight: 1
ReflectionResolution: 1.27→50 Å / Num. obs: 82635 / % possible obs: 99.3 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.023 / Rrim(I) all: 0.08 / Χ2: 0.957 / Net I/σ(I): 8.7 / Num. measured all: 933698
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.27-1.293.40.60536420.6380.3410.7011.12986.8
1.29-1.327.60.64441010.7870.2460.6921.085100
1.32-1.3480.6241810.8080.2310.6631.058100
1.34-1.378.20.58741750.8180.2140.6261.041100
1.37-1.48.60.53341250.8820.1910.5671.025100
1.4-1.438.90.49741970.8970.1740.5271.02100
1.43-1.479.20.42441110.9220.1460.4490.977100
1.47-1.519.60.3741710.9450.1250.3910.978100
1.51-1.55100.30542110.9650.1010.3210.964100
1.55-1.610.40.26941300.9730.0870.2830.97100
1.6-1.6610.90.22941780.9820.0720.2410.943100
1.66-1.7211.40.241000.9860.0620.2090.923100
1.72-1.8120.1641670.9910.0480.1670.928100
1.8-1.912.60.12741910.9950.0370.1320.922100
1.9-2.0213.40.09241650.9970.0260.0960.922100
2.02-2.1714.10.07241250.9980.020.0740.906100
2.17-2.39150.06341870.9980.0170.0650.94100
2.39-2.7415.10.05641600.9980.0150.0570.947100
2.74-3.4517.30.04341600.9990.0110.0440.987100
3.45-5019.10.033415810.0080.0340.86100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KAN

3kan


Resolution: 1.27→41.7 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1729 3992 4.96 %
Rwork0.1371 76441 -
obs0.1388 80433 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.29 Å2 / Biso mean: 17.7263 Å2 / Biso min: 10.39 Å2
Refinement stepCycle: final / Resolution: 1.27→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 30 412 3081
Biso mean--24.29 29.9 -
Num. residues----351
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.27-1.280.2579450.260360264723
1.28-1.30.24491080.19512299240785
1.3-1.320.23911810.17322610279198
1.32-1.330.22781660.16822697286399
1.33-1.350.23811030.167427952898100
1.35-1.370.24321520.157326872839100
1.37-1.390.20071430.154127532896100
1.39-1.410.19821520.147126852837100
1.41-1.440.22941510.148627182869100
1.44-1.460.18891120.135427572869100
1.46-1.490.22511800.130927212901100
1.49-1.520.2051200.125727672887100
1.52-1.550.17281760.122226982874100
1.55-1.580.18191320.112326762808100
1.58-1.620.16071500.113627512901100
1.62-1.660.16611380.122727272865100
1.66-1.70.15411100.120227552865100
1.7-1.750.16861420.114227322874100
1.75-1.810.15991780.131326832861100
1.81-1.870.1541340.127127352869100
1.87-1.950.16341230.124927282851100
1.95-2.040.18011080.12427802888100
2.04-2.150.17241250.14327452870100
2.15-2.280.18821160.1427362852100
2.28-2.460.15221700.142427192889100
2.46-2.70.18541820.153626862868100
2.7-3.090.18811280.156327322860100
3.09-3.90.16521230.139827312854100
3.9-41.70.13781440.12327362880100

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