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

ID or keywords:

Entry

Database: PDB / ID: 8vj2

Title

Crystal Structure of Macrophage migration inhibitory factor-1 (MIF1) from Onchocerca volvulus

Components

Macrophage migration inhibitory factor-1

Keywords

CYTOKINE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Macrophage migration inhibitory factor-1

Function / homology

Macrophage migration inhibitory factor, conserved site / Macrophage migration inhibitory factor family signature. / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily / Macrophage migration inhibitory factor-1

Function and homology information

Biological species

Onchocerca volvulus (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 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-1 (MIF1) from Onchocerca volvulus
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Cooper, A.

History

Deposition	Jan 5, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 17, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vj2.cif.gz	140.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8vj2.ent.gz	110.1 KB	Display	PDB format
PDBx/mmJSON format	8vj2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vj2_validation.pdf.gz	449.5 KB	Display	wwPDB validaton report
Full document	8vj2_full_validation.pdf.gz	451.1 KB	Display
Data in XML	8vj2_validation.xml.gz	13.9 KB	Display
Data in CIF	8vj2_validation.cif.gz	18.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vj/8vj2 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/8vj2	HTTPS FTP

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Related structure data

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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Macrophage migration inhibitory factor-1

B: Macrophage migration inhibitory factor-1

C: Macrophage migration inhibitory factor-1

hetero molecules

43.4 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)	52.441, 91.127, 132.487
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-226- HOH
2	1	A-230- HOH

#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 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: 1.82 Å³/Da / Density % sol: 32.59 %
Crystal grow	Temperature: 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

Crystal

Density Matthews: 1.82 Å³/Da / Density % sol: 32.59 %

Crystal grow

Temperature: 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: ...

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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: 0.9785 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 9, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 1.9→45.45 Å / Num. obs: 25433 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.087 / R_pim(I) all: 0.025 / R_rim(I) all: 0.091 / Χ²: 1.03 / Net I/σ(I): 15 / Num. measured all: 340455
Reflection shell	Resolution: 1.9→1.95 Å / % possible obs: 99.7 % / Redundancy: 14 % / R_merge(I) obs: 1.095 / Num. measured all: 25834 / Num. unique obs: 1843 / CC_1/2: 0.956 / R_pim(I) all: 0.299 / R_rim(I) all: 1.136 / Χ²: 1.06 / Net I/σ(I) obs: 2.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_5177: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.236	1249	4.95 %
R_work	0.2166	-	-
obs	0.2176	25255	99.25 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→45.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2398	0	1	83	2482

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2438
X-RAY DIFFRACTION	f_angle_d	0.7	3290
X-RAY DIFFRACTION	f_dihedral_angle_d	11.25	880
X-RAY DIFFRACTION	f_chiral_restr	0.057	383
X-RAY DIFFRACTION	f_plane_restr	0.005	423

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 (%)
1.9-1.98	0.4181	178	0.3317	2549	X-RAY DIFFRACTION	98
1.98-2.07	0.3221	118	0.2645	2617	X-RAY DIFFRACTION	98
2.07-2.17	0.3255	137	0.2669	2617	X-RAY DIFFRACTION	99
2.17-2.31	0.2421	114	0.2512	2659	X-RAY DIFFRACTION	99
2.31-2.49	0.3014	124	0.2558	2679	X-RAY DIFFRACTION	100
2.49-2.74	0.3278	131	0.2536	2678	X-RAY DIFFRACTION	100
2.74-3.14	0.2552	129	0.2394	2689	X-RAY DIFFRACTION	100
3.14-3.95	0.2176	153	0.2053	2713	X-RAY DIFFRACTION	100
3.95-45.45	0.188	165	0.1777	2805	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	4.8034	-3.2022	-5.6769	4.5186	4.7162	7.0718	0.6201	-0.5076	-0.5679	1.3645	-0.8106	-1.6948	-0.3126	4.1602	-0.0281	0.8315	-0.0404	-0.169	1.1636	0.1676	0.744	9.7562	-6.6366	16.7788
2	4.6329	4.2569	-1.6244	6.1323	-0.1541	4.8179	0.0794	0.2996	0.302	-0.9504	0.0357	0.5902	0.1553	-0.8592	-0.0009	0.3967	0.1299	-0.0086	0.4027	0.02	0.2861	-11.9919	-4.1763	9.2299
3	9.4171	0.1459	5.1823	8.1613	-0.0043	2.8695	-0.5242	0.6675	1.3259	-0.7422	-0.2621	0.1402	-1.5197	-0.0292	0.6674	0.4674	-0.0011	0.0428	0.2663	0.044	0.3403	-4.4847	5.2739	9.8397
4	2.8415	3.9866	0.6042	9.4043	0.2067	3.8396	-0.1149	-0.0291	0.5031	0.5048	-0.0793	-0.0534	-0.0764	0.2182	0.0569	0.404	-0.0016	-0.0087	0.3746	0.0236	0.3454	0.5215	-0.0631	13.4967
5	3.456	-0.5983	-4.0844	9.7332	1.6444	4.9468	0.1166	-0.5178	0.1872	-0.5928	0.0399	0.4415	-0.1215	-1.6636	-0.1247	0.2868	0.0274	-0.0245	0.8146	-0.0026	0.3304	-22.1487	-8.4594	14.2102
6	3.7504	2.4464	-1.214	2.6705	-0.5115	0.4889	-0.2104	-1.2091	-0.3244	0.0877	-0.0923	-0.0658	-0.7154	-0.095	0.3577	0.6925	0.0485	0.0177	0.5761	-0.0014	0.3086	-5.3676	-2.5847	22.2381
7	5.7749	2.3743	-2.7691	5.3721	-6.1624	7.0933	0.302	-1.1878	2.0524	0.2629	0.2813	-0.2876	-2.2417	-0.7976	-0.3459	1.0911	0.257	-0.003	0.5659	-0.1168	0.7303	-11.907	6.7993	17.3735
8	5.7039	2.795	2.494	2.6254	1.823	6.2325	0.2594	-0.2047	0.7364	-0.0121	-0.2173	0.48	-0.6897	-0.9161	-0.028	0.5496	0.2406	0.0459	0.6561	-0.0475	0.3779	-14.0327	-1.1802	19.8293
9	8.238	3.9841	2.4755	6.113	3.5595	2.079	-0.3886	0.5773	0.6889	-0.7817	-0.5199	0.0767	-1.1007	1.0818	0.5105	0.6365	-0.1373	-0.0625	0.6008	0.2015	0.3133	11.3006	-1.9	37.2659
10	2.3694	-3.2732	-0.8248	4.8296	-0.0114	3.969	0.3774	-0.6314	-0.4441	-0.6066	0.4105	0.2794	0.2683	-1.1143	-0.5778	0.4385	-0.1837	-0.068	0.8325	0.1017	0.2996	-21.2609	-18.2401	17.1279
11	2.877	-2.1089	-0.3121	5.8606	3.4186	7.7772	0.1953	-0.4635	-0.1239	-0.3331	0.0983	0.1296	0.7892	-1.3029	0.0967	0.6401	-0.1149	-0.0385	0.6181	-0.0317	0.2674	-14.9119	-19.8295	15.5115
12	8.0472	-4.8079	-2.9786	5.0861	5.62	7.8153	-0.0843	-0.6144	0.2297	-0.2485	0.8175	-0.3808	0.1039	-0.8839	-0.2831	0.5975	-0.1048	-0.0233	0.4877	0.0136	0.2386	-13.0197	-18.2528	25.2642
13	2.1646	-3.1889	-0.4611	4.6601	0.6871	0.1017	0.404	-1.3448	-0.4456	1.4198	-0.4415	0.6616	0.6357	-0.4068	-0.0409	1.2139	-0.7442	-0.226	1.3784	0.2364	0.5932	-21.005	-27.669	22.5285
14	5.5667	2.8925	3.3681	5.2152	4.0522	3.5088	-0.0632	-0.3364	-0.3809	-0.5232	0.2346	0.2033	0.4708	-0.628	-0.1401	1.0461	-0.2978	-0.0615	0.4803	0.0421	0.3794	-12.9301	-26.3283	20.3083
15	3.1937	2.438	-2.965	6.6827	-1.6106	3.1786	-0.0448	-0.1518	0.2468	-0.769	-0.0021	0.7596	0.4247	-1.0443	0.1783	0.5325	-0.0618	-0.0854	0.5567	-0.0126	0.403	-9.5655	-12.0032	45.9404
16	3.1273	1.0331	0.1801	5.5134	-0.626	3.2433	0.0286	0.0684	-0.4315	0.1172	-0.1243	-0.3253	0.7134	0.3359	0.1083	0.5546	0.0771	0.0128	0.2903	-0.0036	0.2649	0.5437	-19.7971	9.8302
17	7.0421	1.521	-3.9633	5.0064	-3.5963	4.7244	-0.1825	-0.2809	0.0146	-0.3229	-0.7286	-1.6415	1.0245	1.403	0.3031	0.7729	0.2977	-0.0043	0.8679	-0.0794	0.478	9.8924	-19.7872	6.8014
18	4.5979	1.7026	1.9916	6.5885	0.1727	3.7012	-0.0504	0.4915	-0.268	-0.3056	0.0266	-0.2503	0.8564	0.5684	0.0948	0.3824	0.1221	0.0259	0.3953	0.0234	0.293	6.4871	-12.9941	11.72
19	5.3888	-5.2996	6.8927	5.5043	-6.9372	8.9855	1.0577	0.9442	-0.3833	-0.0539	-0.7519	-0.1152	1.3117	1.4424	-0.3964	1.049	0.171	-0.0817	0.5413	-0.0425	0.379	7.7584	-25.4157	37.4798

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -3 through 1 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 2 through 16 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 17 through 30 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 31 through 43 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 44 through 57 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 58 through 74 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 75 through 87 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 88 through 102 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 103 through 113 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 0 through 31 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 32 through 57 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 58 through 72 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 73 through 88 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 89 through 102 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 103 through 112 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 0 through 75 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 76 through 88 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 89 through 102 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 103 through 111 )

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