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- PDB-8uz4: Crystal Structure of macrophage migration inhibitory factor (MIF)... -

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Basic information

Entry
Database: PDB / ID: 8uz4
TitleCrystal Structure of macrophage migration inhibitory factor (MIF) from Trichomonas vaginalis (Apo, P41212 form)
ComponentsMACROPHAGE MIGRATION INHIBITORY FACTOR
KeywordsCYTOKINE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / macrophage migration inhibitory factor
Function / homologyphenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily / cytokine activity / extracellular space / L-dopachrome isomerase
Function and homology information
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: Acta Crystallogr.,Sect.F / Year: 2024
Title: Structures of Trichomonas vaginalis macrophage migratory inhibitory factor.
Authors: Srivastava, A. / Nair, A. / Dawson, O.C.O. / Gao, R. / Liu, L. / Craig, J.K. / Battaile, K.P. / Harmon, E.K. / Barrett, L.K. / Van Voorhis, W.C. / Subramanian, S. / Myler, P.J. / Lovell, S. ...Authors: Srivastava, A. / Nair, A. / Dawson, O.C.O. / Gao, R. / Liu, L. / Craig, J.K. / Battaile, K.P. / Harmon, E.K. / Barrett, L.K. / Van Voorhis, W.C. / Subramanian, S. / Myler, P.J. / Lovell, S. / Asojo, O.A. / Darwiche, R.
History
DepositionNov 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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: MACROPHAGE MIGRATION INHIBITORY FACTOR
B: MACROPHAGE MIGRATION INHIBITORY FACTOR
C: MACROPHAGE MIGRATION INHIBITORY FACTOR


Theoretical massNumber of molelcules
Total (without water)44,5283
Polymers44,5283
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-31 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.715, 80.715, 121.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein MACROPHAGE MIGRATION INHIBITORY FACTOR


Mass: 14842.798 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Strain: G3 / Gene: TVAG_219770 / Plasmid: TrvaA.00834.a.UX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2DXT4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Berkeley D5: 100 mM Hepes free acid/ Sodium hydroxide pH 7.5 200 mM Ammonium acetate 25% (w/v) PEG 3350. TrvaA.00834.a.UX1.PW39224 at 35.4 mg/mL. Plate: 13617 well D5 drop 2, Puck: PSL-1907, ...Details: Berkeley D5: 100 mM Hepes free acid/ Sodium hydroxide pH 7.5 200 mM Ammonium acetate 25% (w/v) PEG 3350. TrvaA.00834.a.UX1.PW39224 at 35.4 mg/mL. Plate: 13617 well D5 drop 2, Puck: PSL-1907, Cryo: 20% PEG 200 + 80% crystallant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 9, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→80.71 Å / Num. obs: 16349 / % possible obs: 100 % / Redundancy: 23.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.02 / Rrim(I) all: 0.093 / Χ2: 1.01 / Net I/σ(I): 21.2 / Num. measured all: 379848
Reflection shellResolution: 2.4→2.46 Å / % possible obs: 100 % / Redundancy: 24.6 % / Rmerge(I) obs: 2.689 / Num. measured all: 29417 / Num. unique obs: 1195 / CC1/2: 0.627 / Rpim(I) all: 0.549 / Rrim(I) all: 2.745 / Χ2: 1.01 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→67.17 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2642 816 5.01 %
Rwork0.2453 --
obs0.2463 16289 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→67.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 0 3 2591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082637
X-RAY DIFFRACTIONf_angle_d1.1243556
X-RAY DIFFRACTIONf_dihedral_angle_d4.594355
X-RAY DIFFRACTIONf_chiral_restr0.07396
X-RAY DIFFRACTIONf_plane_restr0.012456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.550.43081310.39742517X-RAY DIFFRACTION100
2.55-2.750.37531140.30462550X-RAY DIFFRACTION100
2.75-3.020.37051450.36042525X-RAY DIFFRACTION100
3.02-3.460.3231400.28942558X-RAY DIFFRACTION100
3.46-4.360.27051270.23852583X-RAY DIFFRACTION100
4.36-67.170.21321590.20222740X-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)
13.9867-1.2192-1.49352.8635-0.07812.97020.0951-0.0082-0.1368-0.06160.177-0.007-0.04710.53130.54460.4103-0.0384-0.0060.8047-0.21980.5881-15.307112.5437-11.7868
24.1273-0.221-1.27682.3544-0.13672.5459-0.31120.2548-0.48510.35280.09570.26180.2559-0.3193-0.00170.40150.01540.0360.4885-0.0610.5231-30.510216.53541.25
32.20031.6655-1.19344.0882-0.0673.42840.4593-0.39610.52870.37920.3711-0.654-0.28490.86371.00380.4312-0.0949-0.09810.8312-0.33180.5914-14.548928.85050.4634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'

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