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- PDB-8dq6: Structure of A. thaliana MIF/D-DT-like protein-1 (MDL1) -

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Basic information

Entry
Database: PDB / ID: 8dq6
TitleStructure of A. thaliana MIF/D-DT-like protein-1 (MDL1)
ComponentsMIF/D-DT-like protein-1
KeywordsCYTOKINE
Function / homology
Function and homology information


phenylpyruvate tautomerase / L-dopachrome isomerase / cytokine activity / extracellular space
Similarity search - Function
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
L-dopachrome isomerase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsManjula, R. / Basquin, J. / Lolis, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci.Signal. / Year: 2023
Title: Plant MDL proteins synergize with the cytokine MIF at CXCR2 and CXCR4 receptors in human cells.
Authors: Spiller, L. / Manjula, R. / Leissing, F. / Basquin, J. / Bourilhon, P. / Sinitski, D. / Brandhofer, M. / Levecque, S. / Gerra, S. / Sabelleck, B. / Zhang, L. / Feederle, R. / Flatley, A. / ...Authors: Spiller, L. / Manjula, R. / Leissing, F. / Basquin, J. / Bourilhon, P. / Sinitski, D. / Brandhofer, M. / Levecque, S. / Gerra, S. / Sabelleck, B. / Zhang, L. / Feederle, R. / Flatley, A. / Hoffmann, A. / Panstruga, R. / Bernhagen, J. / Lolis, E.
History
DepositionJul 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MIF/D-DT-like protein-1
B: MIF/D-DT-like protein-1
C: MIF/D-DT-like protein-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3279
Polymers35,0863
Non-polymers2406
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-98 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.737, 66.737, 132.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein MIF/D-DT-like protein-1 / Light-inducible protein ATLS1-like / Putative light-inducible protein ATLS1 / Tautomerase/MIF ...Light-inducible protein ATLS1-like / Putative light-inducible protein ATLS1 / Tautomerase/MIF superfamily protein


Mass: 11695.446 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MUL3.12, MUL3_12, At5g57170, At5g57170/MUL3_12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LU69
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM Tris, pH 8.0, 0.2 M calcium acetate, 26% PEG8000, 30% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.56→43.53 Å / Num. obs: 46283 / % possible obs: 97.54 % / Redundancy: 20 % / Biso Wilson estimate: 26.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.012 / Rrim(I) all: 0.054 / Net I/σ(I): 31.45
Reflection shellResolution: 1.56→1.62 Å / Rmerge(I) obs: 0.99 / Num. unique obs: 4257 / CC1/2: 0.878 / Rpim(I) all: 0.236 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7KQX

7kqx


Resolution: 1.56→43.53 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 4565 5.01 %
Rwork0.1821 --
obs0.1833 46163 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.56→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 6 134 2425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062342
X-RAY DIFFRACTIONf_angle_d0.8243190
X-RAY DIFFRACTIONf_dihedral_angle_d4.864327
X-RAY DIFFRACTIONf_chiral_restr0.059389
X-RAY DIFFRACTIONf_plane_restr0.005402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.580.29691330.27672461X-RAY DIFFRACTION83
1.58-1.60.27351420.26872664X-RAY DIFFRACTION90
1.6-1.620.29981440.24192778X-RAY DIFFRACTION94
1.62-1.640.23611500.23352822X-RAY DIFFRACTION95
1.64-1.660.23861500.22292847X-RAY DIFFRACTION96
1.66-1.680.35931520.26192876X-RAY DIFFRACTION97
1.68-1.70.30151480.26062891X-RAY DIFFRACTION97
1.7-1.730.26061530.24342892X-RAY DIFFRACTION98
1.73-1.760.25241560.22712967X-RAY DIFFRACTION98
1.76-1.790.20771510.21782866X-RAY DIFFRACTION98
1.79-1.820.26971510.20222893X-RAY DIFFRACTION98
1.82-1.850.23071550.19452953X-RAY DIFFRACTION98
1.85-1.890.20991540.19082895X-RAY DIFFRACTION98
1.89-1.920.37941420.2722777X-RAY DIFFRACTION92
1.92-1.970.21511530.19492874X-RAY DIFFRACTION97
1.97-2.010.2181540.19012902X-RAY DIFFRACTION99
2.01-2.060.19951560.18652942X-RAY DIFFRACTION99
2.06-2.120.20161530.19292927X-RAY DIFFRACTION99
2.12-2.180.22061580.1792954X-RAY DIFFRACTION99
2.18-2.250.22491540.21382918X-RAY DIFFRACTION98
2.25-2.330.22691520.2022894X-RAY DIFFRACTION98
2.33-2.420.19921560.19472951X-RAY DIFFRACTION99
2.42-2.530.1871540.18492936X-RAY DIFFRACTION99
2.53-2.670.20691560.1892998X-RAY DIFFRACTION99
2.67-2.830.22951550.18182939X-RAY DIFFRACTION99
2.83-3.050.2191550.18242948X-RAY DIFFRACTION100
3.05-3.360.19881580.18382969X-RAY DIFFRACTION100
3.36-3.850.19921580.15342956X-RAY DIFFRACTION100
3.85-4.840.16021560.13992962X-RAY DIFFRACTION100
4.85-43.530.17751560.16722969X-RAY DIFFRACTION100

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