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- PDB-9yy9: Macrophage Migration Inhibitory Factor 1 from Heligmosomoides pol... -

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Basic information

Entry
Database: PDB / ID: 9yy9
TitleMacrophage Migration Inhibitory Factor 1 from Heligmosomoides polygyrus
ComponentsMacrophage migration inhibitory factor
KeywordsCYTOKINE / orthologue / parasite / helminth
Function / homologyphenylpyruvate tautomerase activity / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily / cytokine activity / extracellular space / Macrophage migration inhibitory factor
Function and homology information
Biological speciesHeligmosomoides polygyrus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsOrkwis, J.A. / Lolis, E.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Helminth proteins recapitulate key structural motifs of MIF to facilitate immunomodulation of host receptors
Authors: Orkwis, J.A. / Lolis, E.J.
History
DepositionOct 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage migration inhibitory factor


Theoretical massNumber of molelcules
Total (without water)12,6421
Polymers12,6421
Non-polymers00
Water1,31573
1
A: Macrophage migration inhibitory factor

A: Macrophage migration inhibitory factor

A: Macrophage migration inhibitory factor


Theoretical massNumber of molelcules
Total (without water)37,9253
Polymers37,9253
Non-polymers00
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 area7010 Å2
ΔGint-23 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.654, 71.654, 73.125
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Macrophage migration inhibitory factor


Mass: 12641.563 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: H_bakeri_Edinburgh_0011_upd
Source: (gene. exp.) Heligmosomoides polygyrus (invertebrata)
Gene: HPBE_LOCUS13691 / Plasmid: pRSET_A / Details (production host): GeneArt
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A183FYG9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.84 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na Acet 4.5 pH (Buffer), 25 %w/v PEG 3350 (Precipitant)
Temp details: Ambient

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Crygogenic / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2023
RadiationMonochromator: Si(111) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.62→28.51 Å / Num. obs: 17545 / % possible obs: 97.5 % / Redundancy: 4.7 % / CC1/2: 0.965 / Rmerge(I) obs: 0.224 / Net I/σ(I): 9
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 908 / CC1/2: 0.822 / % possible all: 67.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
FAST_DP1.6.2data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→28.51 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.415 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.069
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1747 893 5.09 %
Rwork0.142 16652 -
all0.144 --
obs-17545 97.597 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.455 Å2
Baniso -1Baniso -2Baniso -3
1--0.023 Å2-0.012 Å20 Å2
2---0.023 Å20 Å2
3---0.076 Å2
Refinement stepCycle: LAST / Resolution: 1.62→28.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 0 73 958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.012899
X-RAY DIFFRACTIONr_bond_other_d0.0010.016897
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.6491219
X-RAY DIFFRACTIONr_angle_other_deg0.5971.5662068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9035116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.74456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71310158
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.5241035
X-RAY DIFFRACTIONr_chiral_restr0.0960.2148
X-RAY DIFFRACTIONr_chiral_restr_other0.0350.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02188
X-RAY DIFFRACTIONr_nbd_refined0.2260.2167
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.2748
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2466
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.260
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0370.25
X-RAY DIFFRACTIONr_nbd_other0.180.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1190.29
X-RAY DIFFRACTIONr_mcbond_it4.3291.277467
X-RAY DIFFRACTIONr_mcbond_other4.2031.275467
X-RAY DIFFRACTIONr_mcangle_it5.8892.293582
X-RAY DIFFRACTIONr_mcangle_other5.9122.297583
X-RAY DIFFRACTIONr_scbond_it7.7971.701432
X-RAY DIFFRACTIONr_scbond_other7.7891.705433
X-RAY DIFFRACTIONr_scangle_it10.9542.918637
X-RAY DIFFRACTIONr_scangle_other10.9452.922638
X-RAY DIFFRACTIONr_lrange_it12.36417.3373651
X-RAY DIFFRACTIONr_lrange_other11.98317.063616
X-RAY DIFFRACTIONr_rigid_bond_restr5.36731796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.6580.393530.306895X-RAY DIFFRACTION69.7572
1.658-1.7030.266660.1631214X-RAY DIFFRACTION99.9219
1.703-1.7520.193610.1411186X-RAY DIFFRACTION99.8399
1.752-1.8060.202660.1391151X-RAY DIFFRACTION100
1.806-1.8650.19660.1421124X-RAY DIFFRACTION100
1.865-1.930.223720.1371089X-RAY DIFFRACTION99.7423
1.93-2.0020.179500.1161059X-RAY DIFFRACTION99.9099
2.002-2.0840.193530.121985X-RAY DIFFRACTION99.8077
2.084-2.1760.183460.122976X-RAY DIFFRACTION99.9023
2.176-2.2810.171340.132943X-RAY DIFFRACTION99.5922
2.281-2.4040.157370.131880X-RAY DIFFRACTION99.8911
2.404-2.5490.136520.108821X-RAY DIFFRACTION99.8856
2.549-2.7230.137350.124779X-RAY DIFFRACTION100
2.723-2.9390.16400.14726X-RAY DIFFRACTION100
2.939-3.2160.183470.155674X-RAY DIFFRACTION100
3.216-3.590.179180.154613X-RAY DIFFRACTION100
3.59-4.1340.176360.142528X-RAY DIFFRACTION99.823
4.134-5.0370.08190.143451X-RAY DIFFRACTION99.7877
5.037-7.0160.221330.181355X-RAY DIFFRACTION100
7.016-28.510.17790.177203X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 2.3326 Å / Origin y: 11.6574 Å / Origin z: 0.9944 Å
111213212223313233
T0.0136 Å20.007 Å20.0021 Å2-0.0051 Å2-0.0033 Å2--0.0147 Å2
L1.0988 °20.0763 °20.2542 °2-0.3412 °20.0746 °2--0.6037 °2
S-0.0095 Å °-0.0412 Å °0.1229 Å °0.0173 Å °-0.0041 Å °0.0199 Å °-0.0813 Å °-0.0532 Å °0.0136 Å °
Refinement TLS groupSelection: ALL

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