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

ID or keywords:

Entry

Database: PDB / ID: 8ur4

Title

Crystal Structure of macrophage migration inhibitory factor (MIF) from Trichomonas vaginalis (I4122 form)

Components

MACROPHAGE MIGRATION INHIBITORY FACTOR

Keywords

CYTOKINE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / macrophage migration inhibitory factor

Function / homology

phenylpyruvate 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 species

Trichomonas vaginalis G3 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal Structure of macrophage migration inhibitory factor (MIF) from Trichomonas vaginalis (I4122 form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Oct 25, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 20, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ur4.cif.gz	149.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ur4.ent.gz	118.1 KB	Display	PDB format
PDBx/mmJSON format	8ur4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ur4_validation.pdf.gz	451.6 KB	Display	wwPDB validaton report
Full document	8ur4_full_validation.pdf.gz	455.6 KB	Display
Data in XML	8ur4_validation.xml.gz	12.9 KB	Display
Data in CIF	8ur4_validation.cif.gz	17.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ur/8ur4 ftp://data.pdbj.org/pub/pdb/validation_reports/ur/8ur4	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: MACROPHAGE MIGRATION INHIBITORY FACTOR

B: MACROPHAGE MIGRATION INHIBITORY FACTOR

C: MACROPHAGE MIGRATION INHIBITORY FACTOR

hetero molecules

44.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

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 number	98
Space group name H-M	I4₁22

#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 interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.33 %
Crystal grow	Temperature: 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

Crystal

Density Matthews: 2.13 Å³/Da / Density % sol: 42.33 %

Crystal grow

Temperature: 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 ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 8, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.55→82.78 Å / Num. obs: 12918 / % possible obs: 100 % / Redundancy: 16.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.129 / R_pim(I) all: 0.033 / R_rim(I) all: 0.133 / Χ²: 1 / Net I/σ(I): 14.8 / Num. measured all: 211801
Reflection shell	Resolution: 2.55→2.62 Å / % possible obs: 100 % / Redundancy: 15.8 % / R_merge(I) obs: 1.956 / Num. measured all: 15124 / Num. unique obs: 955 / CC_1/2: 0.703 / R_pim(I) all: 0.505 / R_rim(I) all: 2.022 / Χ²: 0.97 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_5127: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.28	646	5.01 %
R_work	0.2532	-	-
obs	0.2547	12901	99.96 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.55→82.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2576	0	5	0	2581

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2625
X-RAY DIFFRACTION	f_angle_d	0.501	3538
X-RAY DIFFRACTION	f_dihedral_angle_d	12.193	928
X-RAY DIFFRACTION	f_chiral_restr	0.044	392
X-RAY DIFFRACTION	f_plane_restr	0.004	454

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.55-2.75	0.4158	126	0.3392	2400	X-RAY DIFFRACTION	100
2.75-3.02	0.3761	125	0.3396	2419	X-RAY DIFFRACTION	100
3.02-3.46	0.3642	123	0.3198	2422	X-RAY DIFFRACTION	100
3.46-4.36	0.2519	125	0.241	2453	X-RAY DIFFRACTION	100
4.36-82.78	0.2464	147	0.2129	2561	X-RAY DIFFRACTION	100

Refinement TLS params.

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

ID	L11 (°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)
1	5.171	1.8974	-1.7496	8.9098	-1.1294	6.538	-0.5245	-0.3499	0.1021	-0.0548	0.2213	-0.692	0.8841	-0.0806	0.0082	0.5896	0.1485	-0.0211	0.7262	-0.1964	0.4742	0.8949	10.1661	-29.7019
2	6.4235	1.0055	-2.5052	2.4659	-0.3296	5.1336	0.2189	0.1225	-0.0301	0.1917	-0.0686	-0.3694	-0.3397	1.1059	-0.2581	0.6667	0.0421	-0.0614	0.6102	-0.1957	0.5493	5.0459	14.9	-23.2488
3	6.0471	-1.4367	5.2087	8.9146	3.8697	7.528	-0.3344	-0.4285	-0.4882	-1.5504	-0.5701	0.7487	-1.3263	-1.5249	0.8131	1.1432	-0.1942	0.2161	1.8075	-0.5077	1.3442	-16.8445	19.4302	-11.984
4	7.4801	-1.0073	-1.1929	3.5064	-3.3314	3.9646	0.4249	0.5371	-0.0107	0.1178	-0.6057	0.5708	-1.2755	0.1261	0.2619	0.5682	0.101	-0.0094	0.6696	-0.2445	0.5893	-8.5397	37.3322	-13.5273
5	3.9252	0.5768	-5.1838	4.5437	-2.5644	7.6192	-0.0814	-0.9019	-0.482	1.1948	-0.8301	-0.1679	-1.0054	0.9074	0.5139	0.9347	-0.3608	0.0856	1.0222	-0.1127	0.7325	-6.4379	36.2542	0.2075
6	1.5133	1.832	2.2119	2.274	2.1747	5.001	0.6213	0.2899	-0.7971	-0.5446	-0.5345	0.9725	-0.2522	-2.0747	-0.1707	0.4892	0.2063	-0.1836	1.0369	-0.3128	0.8793	-8.8319	30.1369	-24.4957
7	4.1793	2.086	-2.4727	3.4429	0.7662	3.1453	-0.4769	0.8811	-1.5862	0.1733	-0.9504	1.332	0.7427	-1.7217	0.689	0.6711	-0.2246	0.3777	1.1157	-0.5013	1.3148	-14.5729	28.9425	-9.9834
8	3.9666	0.7894	-1.5334	1.4482	-1.6449	1.9832	-0.3392	0.4009	-0.826	0.0043	-0.8528	0.2156	0.217	0.026	-2.0291	-0.4069	-0.4592	0.093	1.1948	-0.7914	1.3162	-13.5101	26.1756	-16.5458
9	3.9702	3.8715	0.5006	4.1553	1.9203	9.5004	-0.5985	-1.4416	-0.5556	0.5938	-0.1674	1.3346	0.5174	0.588	0.8751	0.9589	-0.0291	-0.0128	1.3009	0.1983	0.9336	5.302	26.7486	0.9024
10	4.5665	-1.0951	-1.2316	4.1241	0.9799	3.7675	-0.1051	-0.2785	-0.0229	-0.1713	0.3372	-0.2785	-0.0062	0.4634	-0.2065	0.3624	0.0362	-0.0136	0.5603	-0.0622	0.4942	9.0767	29.5926	-16.6144
11	5.1082	-1.3382	1.3907	3.7736	-2.2769	3.6827	-0.2806	0.5048	-0.2342	-0.4368	-0.2716	-2.056	0.0075	1.9613	0.5365	0.4799	-0.1088	0.0389	0.7972	-0.1302	0.7197	17.9684	28.1167	-16.0626
12	1.3218	1.6093	1.2224	7.0365	1.3534	1.4211	-0.2653	0.5022	-1.502	-0.1793	-0.0274	-1.0823	1.6999	0.9756	-0.1781	0.7657	0.4018	0.0669	0.8198	-0.3961	0.8464	18.0285	15.4845	-15.1675
13	4.2024	-2.787	0.0775	4.2912	-0.1464	3.076	-0.0309	-0.4942	0.2118	0.2971	0.3998	-0.1667	-0.1562	0.1536	-0.2834	0.5183	-0.0556	-0.0208	0.6158	-0.0735	0.4873	4.266	33.8935	-13.0181
14	9.1456	-0.7091	0.29	2.269	-3.7198	8.8079	0.1348	-1.2422	-0.3959	0.6577	0.0871	-0.6618	0.1505	0.4823	-0.2058	0.4674	-0.0246	-0.0756	0.6292	-0.0737	0.4572	11.2486	28.5037	-5.0014
15	1.3264	0.8301	-1.8971	0.703	-1.4235	3.0292	0.7739	-0.2302	-0.683	-1.0644	0.6433	0.5363	-0.0765	-0.1497	-0.7419	1.4457	-0.2415	0.1094	1.3962	0.1747	1.1525	6.2425	8.835	-19.4085
16	4.8953	-1.218	1.9207	2.6852	1.7197	2.814	-0.6622	0.642	-0.612	-0.6165	-0.3195	0.1005	0.2504	-0.8749	0.7188	0.6413	-0.0214	-0.0368	0.8416	-0.3167	0.6905	-0.5501	22.9946	-27.0574
17	7.4325	4.2315	-2.8433	3.5311	-4.1732	7.0004	-0.4002	0.4629	-0.2241	-1.1863	0.1501	0.0918	0.8512	-1.3398	0.227	0.7771	0.0815	-0.1398	0.7738	-0.2746	0.5218	-6.0933	18.5329	-33.1228
18	3.5032	1.1825	-2.6112	1.0104	-0.8117	1.9557	0.244	-0.488	0.2837	-0.0066	0.5432	0.2873	0.1668	-1.0967	0.7372	0.1867	-0.088	-0.2786	1.064	-0.3462	1.4275	-15.6575	14.0861	-25.7369
19	7.8401	-0.1367	1.5578	4.5915	-0.1892	3.4111	0.6831	0.6425	0.4993	-0.7484	-0.8318	0.5047	0.1867	-0.0638	0.1329	0.5003	0.0589	0.0821	0.7142	-0.2633	0.4773	7.8338	24.2162	-25.9254
20	5.2747	4.3055	-5.0969	4.2539	-4.435	5.0212	1.0465	-0.6726	-0.3081	0.29	-0.5182	0.9455	-0.4578	0.2119	-0.317	0.572	-0.0099	0.0361	0.7295	-0.0922	0.5856	-3.2078	14.9186	-19.4507

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 84 through 101 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 102 through 115 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 116 through 127 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 13 through 45 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 46 through 52 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 53 through 71 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 72 through 101 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 102 through 115 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 116 through 127 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 13 through 26 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 27 through 45 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 46 through 52 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 53 through 77 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 78 through 113 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 114 through 127 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 13 through 26 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 27 through 45 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 46 through 52 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 53 through 71 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 72 through 83 )

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