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- PDB-9mf3: Crystal Structure of macrophage migration inhibitory factor from ... -

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Basic information

Entry
Database: PDB / ID: 9mf3
TitleCrystal Structure of macrophage migration inhibitory factor from Plasmodium knowlesi
ComponentsL-dopachrome isomerase
KeywordsCYTOKINE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / macrophage migration inhibitory factor / TPlasmodium knowlesi
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 / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / L-dopachrome isomerase
Similarity search - Component
Biological speciesPlasmodium knowlesi strain H (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 knowlesi
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionDec 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 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
B: L-dopachrome isomerase
C: L-dopachrome isomerase
D: L-dopachrome isomerase
E: L-dopachrome isomerase
F: L-dopachrome isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,88810
Polymers90,6976
Non-polymers1914
Water1629
1
A: L-dopachrome isomerase
B: L-dopachrome isomerase
C: L-dopachrome isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4445
Polymers45,3493
Non-polymers962
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-35 kcal/mol
Surface area13220 Å2
MethodPISA
2
D: L-dopachrome isomerase
E: L-dopachrome isomerase
F: L-dopachrome isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4445
Polymers45,3493
Non-polymers962
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-35 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.171, 134.171, 132.695
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
L-dopachrome isomerase / L-dopachrome tautomerase / Phenylpyruvate tautomerase


Mass: 15116.226 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium knowlesi strain H (eukaryote)
Gene: PKNH_1448700 / Plasmid: PlknA.00834.a.UX11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A384LDV6, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystal Screen HT B12: 0.2M CaCl2, 0.1M NaAc/HAC pH 4.6, 20% iso-propanol. PlknA.00834.a.UX1.PW39225 at 23.5 mg/mL. plate Liu-S-144 B1. Puck: PSL-0508, Cryo: 30% glycerol + 70% 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: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 28, 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: 2.75→47.44 Å / Num. obs: 32136 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.042 / Rrim(I) all: 0.153 / Χ2: 1.07 / Net I/σ(I): 15.5 / Num. measured all: 424806
Reflection shellResolution: 2.75→2.82 Å / % possible obs: 100 % / Redundancy: 13 % / Rmerge(I) obs: 1.932 / Num. measured all: 30250 / Num. unique obs: 2327 / CC1/2: 0.575 / Rpim(I) all: 0.554 / Rrim(I) all: 2.01 / Χ2: 0.95 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIXdev_5508refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→47.44 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 1617 5.04 %
Rwork0.1984 --
obs0.1998 32076 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5421 0 10 9 5440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055516
X-RAY DIFFRACTIONf_angle_d0.8627398
X-RAY DIFFRACTIONf_dihedral_angle_d12.4852040
X-RAY DIFFRACTIONf_chiral_restr0.048826
X-RAY DIFFRACTIONf_plane_restr0.006961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.830.34081290.3012497X-RAY DIFFRACTION100
2.83-2.920.33251330.27472480X-RAY DIFFRACTION100
2.92-3.030.32411380.26652478X-RAY DIFFRACTION100
3.03-3.150.27441370.27082503X-RAY DIFFRACTION100
3.15-3.290.24281250.23922509X-RAY DIFFRACTION100
3.29-3.460.2571550.23052487X-RAY DIFFRACTION100
3.46-3.680.3151400.22562519X-RAY DIFFRACTION100
3.68-3.970.25691220.20222546X-RAY DIFFRACTION100
3.97-4.360.17291550.16192519X-RAY DIFFRACTION100
4.36-50.17381050.14852593X-RAY DIFFRACTION100
5-6.290.20391620.18472566X-RAY DIFFRACTION100
6.29-47.440.18791160.18242762X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.85572.6269-3.7692.9734-3.58075.3606-1.88671.03030.609-0.18671.3120.01310.5056-0.40960.68880.66060.1492-0.07120.6115-0.11690.5323-45.9584-16.3887-23.2755
21.7243-0.9215-1.1291.39990.17618.25430.12240.35690.5320.44920.00550.70410.4477-0.96030.07380.394-0.07110.02020.4788-0.0230.7597-57.1404-12.6226-5.0622
38.26691.2044-4.65587.0744-3.74985.1404-0.34741.01880.1552-0.49530.35280.36880.9966-1.5256-0.21380.4505-0.1262-0.08290.7412-0.15870.6416-61.1145-14.6006-16.026
47.99191.19511.02934.2092-4.4185.8462-0.28811.08970.866-0.73580.1964-0.2187-0.32851.41010.1470.6262-0.0211-0.11340.7899-0.15030.5952-52.8017-17.4194-24.6373
52.40950.3823.01913.9610.2324.06910.2766-0.6247-0.07490.53660.1229-0.19960.3440.0828-0.37120.4149-0.0549-0.03170.56190.04950.6537-56.1458-8.5720.7756
68.4196-2.2172-2.96063.9950.34828.39760.25431.27280.0056-0.5631-0.17510.0596-0.8608-0.41510.04420.4852-0.0066-0.07970.4519-0.0310.4699-54.9112-4.9994-15.9428
76.38392.1529-4.56264.76050.88697.4821-0.21640.47360.69720.00820.25640.40960.1959-0.20370.07050.37830.0399-0.09390.5097-0.09170.5543-56.453-3.1711-8.2311
81.67830.85460.32032.04650.50354.77910.22360.40870.17810.0775-0.1113-0.8801-0.09280.44980.02740.77670.03020.02240.8450.05730.78-37.6652-17.6595-20.3006
97.0911.5137-4.61132.481-2.87624.66080.4393-0.7947-0.34190.89360.4716-2.33990.04952.246-0.56870.46470.1172-0.16280.9219-0.24180.9248-26.7253-12.4146-0.5925
109.09222.1061-2.16984.8555-1.45462.87-0.4594-1.0168-1.1121-0.5007-0.2327-0.39440.677-0.15460.47520.61440.05990.09880.48080.00160.6254-45.1884-24.2191-4.0942
113.44672.6854-2.4275.2607-1.46555.59220.2517-0.4227-0.95430.2564-0.5054-0.47040.55050.50450.29120.59690.1012-0.0910.44440.03010.6737-33.9813-27.5721-2.1674
127.896-0.4617-1.00684.6684-0.744.078-0.9814-0.48580.68120.18160.36680.0422-0.0695-0.08810.4970.34690.1144-0.02470.3337-0.08840.593-34.0015-20.3346-0.0831
132.817-2.1919-1.833.9760.09869.8906-0.02770.1057-0.77420.03540.2070.636-0.0969-0.9223-0.25940.5142-0.0214-0.03520.4673-0.05720.8963-54.3767-23.517-11.5206
146.12121.42620.52875.2468-0.09722.5693-0.12330.3988-0.0648-0.45930.0745-0.77290.31390.3504-0.0310.40480.11730.0340.49840.01890.579-34.1279-21.5429-11.8498
152.99641.73531.14453.6729-2.84576.2438-0.27770.6063-0.2317-0.99250.02340.03171.04570.25720.24740.51220.0946-0.00790.474-0.07540.6097-41.9213-23.2374-13.6808
166.03162.30941.18453.2472-0.3212.1131-0.27280.20920.3743-0.67230.7026-1.1638-0.0854-0.50250.03190.7374-0.0170.1360.6231-0.09210.9476-29.6728-4.12050.7909
172.4755-2.41610.28468.1079-0.30653.6473-0.0514-0.15750.11860.29480.06310.1621-0.0475-0.1438-0.02880.359-0.00870.02720.4513-0.04160.4329-45.9728-6.45266.5939
183.3582-2.10430.98027.4965-1.48956.3306-0.2724-0.42140.74960.16050.2983-0.6708-0.74510.246-0.15660.43950.00940.02320.5092-0.16030.7608-38.145-0.58364.6206
194.5323-0.4216-2.22487.9984-1.6733.95460.0571-0.8005-0.0039-0.056-0.0437-0.54190.8271.0742-0.38250.40730.08650.02420.605-0.1170.5804-36.2284-8.35136.417
202.1227-0.7415-0.71117.67340.82775.57420.284-0.64220.7305-0.367-0.2504-0.4935-0.62740.38740.03990.6716-0.04560.01160.59840.01450.7959-51.0813.2324-12.3793
211.72092.00980.71223.15981.78441.76989.299519.95431.7779-9.3711-5.13081.7215-5.5328-13.8734-4.33760.92780.4564-0.18221.36480.0581.3523-48.97347.592-16.4761
224.31571.128-2.27590.8837-0.27549.771-0.0135-0.7653-0.45040.2781-0.29740.00260.170.29080.09810.702-0.12530.00290.71520.03270.7078-72.742-15.990718.6357
234.7390.2522-0.07014.5816-1.58511.62040.1133-0.0395-1.02990.14640.76610.89441.9191-3.1617-0.62360.9002-0.29970.13130.7930.04820.7546-76.3661-19.300821.18
243.7976-0.8782.05216.02091.69755.64070.0972-0.3732-0.5755-0.5798-0.22790.2837-0.5491-1.1034-0.14620.6342-0.04090.08830.7644-0.12080.6126-76.4422-7.15261.0672
259.06931.595-1.47014.1541-2.06713.47360.4126-1.04860.09731.1506-0.1815-0.2318-1.3143-0.5830.1340.8012-0.12510.090.8195-0.01840.552-77.841-7.749221.2793
265.06610.3591-1.65496.7092-1.35126.8958-0.27450.17831.14280.39310.5176-0.4032-0.3214-0.5022-0.04760.5502-0.01790.07690.75530.05610.4878-76.4713-5.264313.3816
275.23394.9198-0.71987.6802-0.05876.79210.67141.1641-0.9850.6432-1.3244-0.9466-1.8041-1.87350.48571.2125-0.2790.2241.74240.07310.9502-91.7452-23.897925.6052
283.1556-0.36880.22967.1807-1.17986.42420.0369-0.15-0.3895-0.81820.14520.19090.3113-1.164-0.26550.5511-0.1710.05081.04760.02460.5452-86.6522-11.2201-1.4488
290.74010.49220.62962.773-0.5032.7126-0.051-0.1679-0.0443-0.10920.34930.7152-0.1686-1.6101-0.23660.7424-0.1110.07861.59480.08610.9177-92.9089-7.45224.0971
306.3913-1.47211.86094.735-0.29216.22990.42821.23030.8634-1.1944-0.09171.95011.771-1.6395-0.2671.0208-0.5347-0.11461.18910.21011.1926-92.9617-23.96099.2015
316.28611.5375-1.24742.3378-1.76562.7084-0.0841.0293-1.2077-0.18540.31430.73362.7809-1.6898-0.14411.573-0.7723-0.25241.34240.04591.1574-90.528-34.00597.715
325.89111.1991-1.5321.7935-1.46852.4066-0.72752.1077-0.9110.73341.1697-0.216-1.5605-0.1403-0.37891.1952-0.7284-0.52921.8930.30871.3432-104.0764-28.05135.6477
335.287-0.9809-0.4844.4247-0.0931.37510.3176-0.57570.97861.01070.03130.7131.3722-0.7434-0.28211.6334-1.1296-0.01210.47160.15631.1003-85.5551-26.34386.0593
341.14130.84541.11533.9809-2.13338.8360.1063-0.9373-0.6247-0.4213-0.3137-1.2721.3646-0.53980.24521.1037-0.3318-0.0330.84710.13810.7978-74.3711-25.970116.6749
357.88272.0772.95513.998-0.03576.35020.2479-0.10980.34120.4525-0.64730.73530.889-2.3002-0.10921.2656-0.46990.12571.6733-0.23741.0703-90.4076-23.073514.5344
363.98-0.25412.09313.98721.79222.0775-0.0186-0.9926-0.45150.95010.27511.04181.7226-2.4632-0.14571.436-0.63140.1661.67520.36181.1036-96.0037-30.416318.6423
375.8221-1.62711.40773.44642.93446.56680.8327-0.0675-0.720.5879-0.86241.02471.9033-0.6176-0.03511.316-0.3750.05181.38550.32460.9169-86.5591-28.490119.0294
384.3605-0.0266-0.09166.49330.5189.3448-0.3177-1.75270.3794-0.49011.5450.29211.26570.3065-0.94230.7915-0.2873-0.14732.35070.16351.2213-102.662-12.32134.8623
391.99991.99982.000121.99992-7.2755-4.82798.2177-7.18035.349511.6277-25.51342.50061.76752.05430.80850.37242.57331.44041.1742-108.5893-9.22046.5736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 2 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3 through 13 )
3X-RAY DIFFRACTION3chain 'A' and (resid 14 through 32 )
4X-RAY DIFFRACTION4chain 'A' and (resid 33 through 39 )
5X-RAY DIFFRACTION5chain 'A' and (resid 40 through 58 )
6X-RAY DIFFRACTION6chain 'A' and (resid 59 through 88 )
7X-RAY DIFFRACTION7chain 'A' and (resid 89 through 102 )
8X-RAY DIFFRACTION8chain 'A' and (resid 103 through 116 )
9X-RAY DIFFRACTION9chain 'B' and (resid -2 through 2 )
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 13 )
11X-RAY DIFFRACTION11chain 'B' and (resid 14 through 32 )
12X-RAY DIFFRACTION12chain 'B' and (resid 33 through 45 )
13X-RAY DIFFRACTION13chain 'B' and (resid 46 through 58 )
14X-RAY DIFFRACTION14chain 'B' and (resid 59 through 88 )
15X-RAY DIFFRACTION15chain 'B' and (resid 89 through 102 )
16X-RAY DIFFRACTION16chain 'B' and (resid 103 through 116 )
17X-RAY DIFFRACTION17chain 'C' and (resid -2 through 58 )
18X-RAY DIFFRACTION18chain 'C' and (resid 59 through 88 )
19X-RAY DIFFRACTION19chain 'C' and (resid 89 through 102 )
20X-RAY DIFFRACTION20chain 'C' and (resid 103 through 115 )
21X-RAY DIFFRACTION21chain 'C' and (resid 116 through 116 )
22X-RAY DIFFRACTION22chain 'D' and (resid -2 through 32 )
23X-RAY DIFFRACTION23chain 'D' and (resid 33 through 45 )
24X-RAY DIFFRACTION24chain 'D' and (resid 46 through 58 )
25X-RAY DIFFRACTION25chain 'D' and (resid 59 through 88 )
26X-RAY DIFFRACTION26chain 'D' and (resid 89 through 102 )
27X-RAY DIFFRACTION27chain 'D' and (resid 103 through 115 )
28X-RAY DIFFRACTION28chain 'E' and (resid -1 through 58 )
29X-RAY DIFFRACTION29chain 'E' and (resid 59 through 115 )
30X-RAY DIFFRACTION30chain 'F' and (resid 0 through 8 )
31X-RAY DIFFRACTION31chain 'F' and (resid 9 through 32 )
32X-RAY DIFFRACTION32chain 'F' and (resid 33 through 39 )
33X-RAY DIFFRACTION33chain 'F' and (resid 40 through 45 )
34X-RAY DIFFRACTION34chain 'F' and (resid 46 through 58 )
35X-RAY DIFFRACTION35chain 'F' and (resid 59 through 65 )
36X-RAY DIFFRACTION36chain 'F' and (resid 66 through 88 )
37X-RAY DIFFRACTION37chain 'F' and (resid 89 through 102 )
38X-RAY DIFFRACTION38chain 'F' and (resid 103 through 115 )
39X-RAY DIFFRACTION39chain 'F' and (resid 116 through 116 )

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