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- PDB-9b0m: Crystal structure of Macrophage migration inhibitory factor from ... -

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Basic information

Entry
Database: PDB / ID: 9b0m
TitleCrystal structure of Macrophage migration inhibitory factor from Plasmodium vivax
ComponentsL-dopachrome isomerase
KeywordsCYTOKINE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Macrophage migration inhibitory factor / MIF / L-dopachrome isomerase / LIPID TRANSPORT
Function / homologyphenylpyruvate tautomerase / L-dopachrome isomerase / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily / cytokine activity / extracellular space / DI(HYDROXYETHYL)ETHER / L-dopachrome isomerase
Function and homology information
Biological speciesPlasmodium vivax Sal-1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Macrophage migration inhibitory factor from Plasmodium vivax
Authors: Lovell, S. / Liu, L. / Cooper, A. / Battaile, K.P.
History
DepositionMar 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-dopachrome isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1193
Polymers14,9211
Non-polymers1982
Water34219
1
A: L-dopachrome isomerase
hetero molecules

A: L-dopachrome isomerase
hetero molecules

A: L-dopachrome isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3579
Polymers44,7633
Non-polymers5956
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area4620 Å2
ΔGint-7 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.457, 75.457, 36.947
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-317-

HOH

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Components

#1: Protein L-dopachrome isomerase / L-dopachrome tautomerase / Phenylpyruvate tautomerase


Mass: 14920.837 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax Sal-1 (eukaryote) / Gene: PVX_124095 / Plasmid: PlviB.00834.a.UX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A5K093, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.04 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Index D5: 25% w/v Polyethylene glycol 3,350, 0.1 M Sodium acetate trihydrate pH 4.5, PlviB.00834.a.UX1.PW39232 at 12 mg/mL. plate 13719 D5 drop 3. Puck: PSL-0913, Cryo: 80% crystallant + 20% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 19, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.8→37.73 Å / Num. obs: 11324 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.034 / Rrim(I) all: 0.124 / Χ2: 1.02 / Net I/σ(I): 11.2 / Num. measured all: 154623
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 1.878 / Num. measured all: 9558 / Num. unique obs: 677 / CC1/2: 0.664 / Rpim(I) all: 0.514 / Rrim(I) all: 1.948 / Χ2: 1.13 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(dev_5267: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→37.73 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2176 534 4.73 %
Rwork0.1868 --
obs0.1883 11293 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→37.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms734 0 13 19 766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009764
X-RAY DIFFRACTIONf_angle_d0.9441023
X-RAY DIFFRACTIONf_dihedral_angle_d16.479288
X-RAY DIFFRACTIONf_chiral_restr0.05117
X-RAY DIFFRACTIONf_plane_restr0.007130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.980.28661230.28292664X-RAY DIFFRACTION100
1.98-2.270.25591290.19642689X-RAY DIFFRACTION100
2.27-2.860.24951360.23142686X-RAY DIFFRACTION100
2.86-37.730.20091460.1672720X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.68441.31090.3322.1833-2.63866.51390.02711.2241-0.1925-0.9283-0.22-0.295-0.4391.16030.06160.7379-0.03010.11070.7307-0.09690.47354.921832.8505-8.3029
28.8334-0.6542-0.99586.5834-0.80066.4567-0.26990.8634-1.1781-0.5423-0.05380.08981.1829-0.31830.3250.6532-0.01540.06190.3604-0.14560.53353.424225.2741-2.8933
35.7283-0.7857-0.98283.8656-0.40225.9128-0.0793-0.1681-0.3429-0.0864-0.1909-0.25640.42380.7430.30770.32650.09950.01250.3620.03630.349310.079131.97191.7139
43.8235-1.8311-4.26194.80821.19155.21940.29250.34340.0559-0.3836-0.2986-0.32650.03390.15430.05650.37230.1207-0.00090.4730.0250.388512.383637.2258-1.4379
58.35171.11352.92319.3832.4457.35380.2923-0.4107-0.01390.314-0.4112-0.03370.522-0.79140.12090.3411-0.0721-0.00040.44270.01590.3492-8.701332.77025.0324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 59 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 101 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 32 )
4X-RAY DIFFRACTION4chain 'A' and (resid 33 through 45 )
5X-RAY DIFFRACTION5chain 'A' and (resid 46 through 58 )

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