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- PDB-8ur4: Crystal Structure of macrophage migration inhibitory factor (MIF)... -

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Basic information

Entry
Database: PDB / ID: 8ur4
TitleCrystal Structure of macrophage migration inhibitory factor (MIF) from Trichomonas vaginalis (I4122 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 G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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
DepositionOct 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MACROPHAGE MIGRATION INHIBITORY FACTOR
B: MACROPHAGE MIGRATION INHIBITORY FACTOR
C: MACROPHAGE MIGRATION INHIBITORY FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7068
Polymers44,5283
Non-polymers1775
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-69 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.871, 109.871, 125.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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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 G3 (eukaryote) / Gene: TVAG_219770 / Plasmid: TrvaA.00834.a.UX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2DXT4
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestN
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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Index A4: 0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate. TrvaA.00834.a.UX1.PW39224 at 35.4 mg/mL. 5 mM Sodium 4-OH-phenyl-pyruvate added to the protien prior to crystallization. No electron ...Details: Index A4: 0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate. TrvaA.00834.a.UX1.PW39224 at 35.4 mg/mL. 5 mM Sodium 4-OH-phenyl-pyruvate added to the protien prior to crystallization. No electron density for the ligand was observed. Plate: 13644 well A4 drop 1, Puck: PSL-0107, Cryo: 2.5M Lithium sulfate

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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 8, 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: 2.55→82.78 Å / Num. obs: 12918 / % possible obs: 100 % / Redundancy: 16.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.033 / Rrim(I) all: 0.133 / Χ2: 1 / Net I/σ(I): 14.8 / Num. measured all: 211801
Reflection shellResolution: 2.55→2.62 Å / % possible obs: 100 % / Redundancy: 15.8 % / Rmerge(I) obs: 1.956 / Num. measured all: 15124 / Num. unique obs: 955 / CC1/2: 0.703 / Rpim(I) all: 0.505 / Rrim(I) all: 2.022 / Χ2: 0.97 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5127: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→82.78 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 646 5.01 %
Rwork0.2532 --
obs0.2547 12901 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→82.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 5 0 2581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032625
X-RAY DIFFRACTIONf_angle_d0.5013538
X-RAY DIFFRACTIONf_dihedral_angle_d12.193928
X-RAY DIFFRACTIONf_chiral_restr0.044392
X-RAY DIFFRACTIONf_plane_restr0.004454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.750.41581260.33922400X-RAY DIFFRACTION100
2.75-3.020.37611250.33962419X-RAY DIFFRACTION100
3.02-3.460.36421230.31982422X-RAY DIFFRACTION100
3.46-4.360.25191250.2412453X-RAY DIFFRACTION100
4.36-82.780.24641470.21292561X-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)
15.1711.8974-1.74968.9098-1.12946.538-0.5245-0.34990.1021-0.05480.2213-0.6920.8841-0.08060.00820.58960.1485-0.02110.7262-0.19640.47420.894910.1661-29.7019
26.42351.0055-2.50522.4659-0.32965.13360.21890.1225-0.03010.1917-0.0686-0.3694-0.33971.1059-0.25810.66670.0421-0.06140.6102-0.19570.54935.045914.9-23.2488
36.0471-1.43675.20878.91463.86977.528-0.3344-0.4285-0.4882-1.5504-0.57010.7487-1.3263-1.52490.81311.1432-0.19420.21611.8075-0.50771.3442-16.844519.4302-11.984
47.4801-1.0073-1.19293.5064-3.33143.96460.42490.5371-0.01070.1178-0.60570.5708-1.27550.12610.26190.56820.101-0.00940.6696-0.24450.5893-8.539737.3322-13.5273
53.92520.5768-5.18384.5437-2.56447.6192-0.0814-0.9019-0.4821.1948-0.8301-0.1679-1.00540.90740.51390.9347-0.36080.08561.0222-0.11270.7325-6.437936.25420.2075
61.51331.8322.21192.2742.17475.0010.62130.2899-0.7971-0.5446-0.53450.9725-0.2522-2.0747-0.17070.48920.2063-0.18361.0369-0.31280.8793-8.831930.1369-24.4957
74.17932.086-2.47273.44290.76623.1453-0.47690.8811-1.58620.1733-0.95041.3320.7427-1.72170.6890.6711-0.22460.37771.1157-0.50131.3148-14.572928.9425-9.9834
83.96660.7894-1.53341.4482-1.64491.9832-0.33920.4009-0.8260.0043-0.85280.21560.2170.026-2.0291-0.4069-0.45920.0931.1948-0.79141.3162-13.510126.1756-16.5458
93.97023.87150.50064.15531.92039.5004-0.5985-1.4416-0.55560.5938-0.16741.33460.51740.5880.87510.9589-0.0291-0.01281.30090.19830.93365.30226.74860.9024
104.5665-1.0951-1.23164.12410.97993.7675-0.1051-0.2785-0.0229-0.17130.3372-0.2785-0.00620.4634-0.20650.36240.0362-0.01360.5603-0.06220.49429.076729.5926-16.6144
115.1082-1.33821.39073.7736-2.27693.6827-0.28060.5048-0.2342-0.4368-0.2716-2.0560.00751.96130.53650.4799-0.10880.03890.7972-0.13020.719717.968428.1167-16.0626
121.32181.60931.22247.03651.35341.4211-0.26530.5022-1.502-0.1793-0.0274-1.08231.69990.9756-0.17810.76570.40180.06690.8198-0.39610.846418.028515.4845-15.1675
134.2024-2.7870.07754.2912-0.14643.076-0.0309-0.49420.21180.29710.3998-0.1667-0.15620.1536-0.28340.5183-0.0556-0.02080.6158-0.07350.48734.26633.8935-13.0181
149.1456-0.70910.292.269-3.71988.80790.1348-1.2422-0.39590.65770.0871-0.66180.15050.4823-0.20580.4674-0.0246-0.07560.6292-0.07370.457211.248628.5037-5.0014
151.32640.8301-1.89710.703-1.42353.02920.7739-0.2302-0.683-1.06440.64330.5363-0.0765-0.1497-0.74191.4457-0.24150.10941.39620.17471.15256.24258.835-19.4085
164.8953-1.2181.92072.68521.71972.814-0.66220.642-0.612-0.6165-0.31950.10050.2504-0.87490.71880.6413-0.0214-0.03680.8416-0.31670.6905-0.550122.9946-27.0574
177.43254.2315-2.84333.5311-4.17327.0004-0.40020.4629-0.2241-1.18630.15010.09180.8512-1.33980.2270.77710.0815-0.13980.7738-0.27460.5218-6.093318.5329-33.1228
183.50321.1825-2.61121.0104-0.81171.95570.244-0.4880.2837-0.00660.54320.28730.1668-1.09670.73720.1867-0.088-0.27861.064-0.34621.4275-15.657514.0861-25.7369
197.8401-0.13671.55784.5915-0.18923.41110.68310.64250.4993-0.7484-0.83180.50470.1867-0.06380.13290.50030.05890.08210.7142-0.26330.47737.833824.2162-25.9254
205.27474.3055-5.09694.2539-4.4355.02121.0465-0.6726-0.30810.29-0.51820.9455-0.45780.2119-0.3170.572-0.00990.03610.7295-0.09220.5856-3.207814.9186-19.4507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 84 through 101 )
2X-RAY DIFFRACTION2chain 'B' and (resid 102 through 115 )
3X-RAY DIFFRACTION3chain 'B' and (resid 116 through 127 )
4X-RAY DIFFRACTION4chain 'C' and (resid 13 through 45 )
5X-RAY DIFFRACTION5chain 'C' and (resid 46 through 52 )
6X-RAY DIFFRACTION6chain 'C' and (resid 53 through 71 )
7X-RAY DIFFRACTION7chain 'C' and (resid 72 through 101 )
8X-RAY DIFFRACTION8chain 'C' and (resid 102 through 115 )
9X-RAY DIFFRACTION9chain 'C' and (resid 116 through 127 )
10X-RAY DIFFRACTION10chain 'A' and (resid 13 through 26 )
11X-RAY DIFFRACTION11chain 'A' and (resid 27 through 45 )
12X-RAY DIFFRACTION12chain 'A' and (resid 46 through 52 )
13X-RAY DIFFRACTION13chain 'A' and (resid 53 through 77 )
14X-RAY DIFFRACTION14chain 'A' and (resid 78 through 113 )
15X-RAY DIFFRACTION15chain 'A' and (resid 114 through 127 )
16X-RAY DIFFRACTION16chain 'B' and (resid 13 through 26 )
17X-RAY DIFFRACTION17chain 'B' and (resid 27 through 45 )
18X-RAY DIFFRACTION18chain 'B' and (resid 46 through 52 )
19X-RAY DIFFRACTION19chain 'B' and (resid 53 through 71 )
20X-RAY DIFFRACTION20chain 'B' and (resid 72 through 83 )

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