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- PDB-8vj2: Crystal Structure of Macrophage migration inhibitory factor-1 (MI... -

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Basic information

Entry
Database: PDB / ID: 8vj2
TitleCrystal Structure of Macrophage migration inhibitory factor-1 (MIF1) from Onchocerca volvulus
ComponentsMacrophage migration inhibitory factor-1
KeywordsCYTOKINE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Macrophage migration inhibitory factor-1
Function / homology
Function and homology information


phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / cytokine activity / extracellular space
Similarity search - Function
Macrophage migration inhibitory factor, conserved site / Macrophage migration inhibitory factor family signature. / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
L-dopachrome isomerase
Similarity search - Component
Biological speciesOnchocerca volvulus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Crystal structure of N-terminally hexahistidine-tagged Onchocerca volvulus macrophage migration inhibitory factor-1.
Authors: Kimble, A.D. / Dawson, O.C.O. / Liu, L. / Subramanian, S. / Cooper, A. / Battaile, K. / Craig, J. / Harmon, E. / Myler, P. / Lovell, S. / Asojo, O.A.
History
DepositionJan 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage migration inhibitory factor-1
B: Macrophage migration inhibitory factor-1
C: Macrophage migration inhibitory factor-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3984
Polymers43,3753
Non-polymers231
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-23 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.441, 91.127, 132.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-226-

HOH

21A-230-

HOH

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Components

#1: Protein Macrophage migration inhibitory factor-1


Mass: 14458.456 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Onchocerca volvulus (invertebrata) / Gene: mif1 / Plasmid: OnvoA.00834.a.UX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q963F7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
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: 1.82 Å3/Da / Density % sol: 32.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Berkeley B3: 100 mM Bis-Tris / Hydrochloric acid pH 6.5 400 mM Sodium chloride 30% (w/v) PEG 3350, OnvoA.00834.a.UX1.PW39231 at 20.1 mg/mL. plate 13715 well B3 drop 2. Puck: PSL-1003, Cryo: ...Details: Berkeley B3: 100 mM Bis-Tris / Hydrochloric acid pH 6.5 400 mM Sodium chloride 30% (w/v) PEG 3350, OnvoA.00834.a.UX1.PW39231 at 20.1 mg/mL. plate 13715 well B3 drop 2. Puck: PSL-1003, Cryo: crystallization solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 9, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.9→45.45 Å / Num. obs: 25433 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.025 / Rrim(I) all: 0.091 / Χ2: 1.03 / Net I/σ(I): 15 / Num. measured all: 340455
Reflection shellResolution: 1.9→1.95 Å / % possible obs: 99.7 % / Redundancy: 14 % / Rmerge(I) obs: 1.095 / Num. measured all: 25834 / Num. unique obs: 1843 / CC1/2: 0.956 / Rpim(I) all: 0.299 / Rrim(I) all: 1.136 / Χ2: 1.06 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5177: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.45 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 1249 4.95 %
Rwork0.2166 --
obs0.2176 25255 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 1 83 2482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042438
X-RAY DIFFRACTIONf_angle_d0.73290
X-RAY DIFFRACTIONf_dihedral_angle_d11.25880
X-RAY DIFFRACTIONf_chiral_restr0.057383
X-RAY DIFFRACTIONf_plane_restr0.005423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.980.41811780.33172549X-RAY DIFFRACTION98
1.98-2.070.32211180.26452617X-RAY DIFFRACTION98
2.07-2.170.32551370.26692617X-RAY DIFFRACTION99
2.17-2.310.24211140.25122659X-RAY DIFFRACTION99
2.31-2.490.30141240.25582679X-RAY DIFFRACTION100
2.49-2.740.32781310.25362678X-RAY DIFFRACTION100
2.74-3.140.25521290.23942689X-RAY DIFFRACTION100
3.14-3.950.21761530.20532713X-RAY DIFFRACTION100
3.95-45.450.1881650.17772805X-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)
14.8034-3.2022-5.67694.51864.71627.07180.6201-0.5076-0.56791.3645-0.8106-1.6948-0.31264.1602-0.02810.8315-0.0404-0.1691.16360.16760.7449.7562-6.636616.7788
24.63294.2569-1.62446.1323-0.15414.81790.07940.29960.302-0.95040.03570.59020.1553-0.8592-0.00090.39670.1299-0.00860.40270.020.2861-11.9919-4.17639.2299
39.41710.14595.18238.1613-0.00432.8695-0.52420.66751.3259-0.7422-0.26210.1402-1.5197-0.02920.66740.4674-0.00110.04280.26630.0440.3403-4.48475.27399.8397
42.84153.98660.60429.40430.20673.8396-0.1149-0.02910.50310.5048-0.0793-0.0534-0.07640.21820.05690.404-0.0016-0.00870.37460.02360.34540.5215-0.063113.4967
53.456-0.5983-4.08449.73321.64444.94680.1166-0.51780.1872-0.59280.03990.4415-0.1215-1.6636-0.12470.28680.0274-0.02450.8146-0.00260.3304-22.1487-8.459414.2102
63.75042.4464-1.2142.6705-0.51150.4889-0.2104-1.2091-0.32440.0877-0.0923-0.0658-0.7154-0.0950.35770.69250.04850.01770.5761-0.00140.3086-5.3676-2.584722.2381
75.77492.3743-2.76915.3721-6.16247.09330.302-1.18782.05240.26290.2813-0.2876-2.2417-0.7976-0.34591.09110.257-0.0030.5659-0.11680.7303-11.9076.799317.3735
85.70392.7952.4942.62541.8236.23250.2594-0.20470.7364-0.0121-0.21730.48-0.6897-0.9161-0.0280.54960.24060.04590.6561-0.04750.3779-14.0327-1.180219.8293
98.2383.98412.47556.1133.55952.079-0.38860.57730.6889-0.7817-0.51990.0767-1.10071.08180.51050.6365-0.1373-0.06250.60080.20150.313311.3006-1.937.2659
102.3694-3.2732-0.82484.8296-0.01143.9690.3774-0.6314-0.4441-0.60660.41050.27940.2683-1.1143-0.57780.4385-0.1837-0.0680.83250.10170.2996-21.2609-18.240117.1279
112.877-2.1089-0.31215.86063.41867.77720.1953-0.4635-0.1239-0.33310.09830.12960.7892-1.30290.09670.6401-0.1149-0.03850.6181-0.03170.2674-14.9119-19.829515.5115
128.0472-4.8079-2.97865.08615.627.8153-0.0843-0.61440.2297-0.24850.8175-0.38080.1039-0.8839-0.28310.5975-0.1048-0.02330.48770.01360.2386-13.0197-18.252825.2642
132.1646-3.1889-0.46114.66010.68710.10170.404-1.3448-0.44561.4198-0.44150.66160.6357-0.4068-0.04091.2139-0.7442-0.2261.37840.23640.5932-21.005-27.66922.5285
145.56672.89253.36815.21524.05223.5088-0.0632-0.3364-0.3809-0.52320.23460.20330.4708-0.628-0.14011.0461-0.2978-0.06150.48030.04210.3794-12.9301-26.328320.3083
153.19372.438-2.9656.6827-1.61063.1786-0.0448-0.15180.2468-0.769-0.00210.75960.4247-1.04430.17830.5325-0.0618-0.08540.5567-0.01260.403-9.5655-12.003245.9404
163.12731.03310.18015.5134-0.6263.24330.02860.0684-0.43150.1172-0.1243-0.32530.71340.33590.10830.55460.07710.01280.2903-0.00360.26490.5437-19.79719.8302
177.04211.521-3.96335.0064-3.59634.7244-0.1825-0.28090.0146-0.3229-0.7286-1.64151.02451.4030.30310.77290.2977-0.00430.8679-0.07940.4789.8924-19.78726.8014
184.59791.70261.99166.58850.17273.7012-0.05040.4915-0.268-0.30560.0266-0.25030.85640.56840.09480.38240.12210.02590.39530.02340.2936.4871-12.994111.72
195.3888-5.29966.89275.5043-6.93728.98551.05770.9442-0.3833-0.0539-0.7519-0.11521.31171.4424-0.39641.0490.171-0.08170.5413-0.04250.3797.7584-25.415737.4798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 1 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2 through 16 )
3X-RAY DIFFRACTION3chain 'A' and (resid 17 through 30 )
4X-RAY DIFFRACTION4chain 'A' and (resid 31 through 43 )
5X-RAY DIFFRACTION5chain 'A' and (resid 44 through 57 )
6X-RAY DIFFRACTION6chain 'A' and (resid 58 through 74 )
7X-RAY DIFFRACTION7chain 'A' and (resid 75 through 87 )
8X-RAY DIFFRACTION8chain 'A' and (resid 88 through 102 )
9X-RAY DIFFRACTION9chain 'A' and (resid 103 through 113 )
10X-RAY DIFFRACTION10chain 'B' and (resid 0 through 31 )
11X-RAY DIFFRACTION11chain 'B' and (resid 32 through 57 )
12X-RAY DIFFRACTION12chain 'B' and (resid 58 through 72 )
13X-RAY DIFFRACTION13chain 'B' and (resid 73 through 88 )
14X-RAY DIFFRACTION14chain 'B' and (resid 89 through 102 )
15X-RAY DIFFRACTION15chain 'B' and (resid 103 through 112 )
16X-RAY DIFFRACTION16chain 'C' and (resid 0 through 75 )
17X-RAY DIFFRACTION17chain 'C' and (resid 76 through 88 )
18X-RAY DIFFRACTION18chain 'C' and (resid 89 through 102 )
19X-RAY DIFFRACTION19chain 'C' and (resid 103 through 111 )

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