PDB-3hof: Structure of macrophage migration inhibitory factor (MIF) with ca...

ID or keywords:

Entry

Database: PDB / ID: 3hof

Title

Structure of macrophage migration inhibitory factor (MIF) with caffeic acid at 1.9A resolution

Components

Macrophage migration inhibitory factor

Keywords

ISOMERASE / Homotrimer / cytokine / inflammatory response / tautomerase / Phosphoprotein

Function / homology

Function and homology information

positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate secretion / negative regulation of myeloid cell apoptotic process ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate secretion / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / carboxylic acid metabolic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of protein metabolic process / prostaglandin biosynthetic process / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / positive regulation of protein kinase A signaling / protein homotrimerization / negative regulation of cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / positive regulation of B cell proliferation / positive regulation of phosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of cell migration / positive regulation of cytokine production / cytokine activity / Cell surface interactions at the vascular wall / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / protease binding / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Crawley, L. / Barker, J. / Cheng, R.K.Y. / Wood, M. / Felicetti, B.

Citation

Journal: To be Published
Title: Structure of macrophage migration inhibitory factor (MIF) with caffeic acid at 1.9A resolution
Authors: Crawley, L. / Barker, J. / Cheng, R.K.Y. / Wood, M. / Felicetti, B.

History

Deposition	Jun 2, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 16, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3hof.cif.gz	89.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3hof.ent.gz	69.1 KB	Display	PDB format
PDBx/mmJSON format	3hof.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ho/3hof ftp://data.pdbj.org/pub/pdb/validation_reports/ho/3hof	HTTPS FTP

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Related structure data

Related structure data	1ca7S S: Starting model for refinement
Similar structure data	3l5p-d 3l5v-d 3l5t-d 3wnr-d 4osf-d 3l5u-d 3jsf-d 3l5s-d 3jtu-d 4grr-d Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#128 - Aug 2010 Interferons similarity (1) #94 - Oct 2007 Superoxide Dismutase similarity (1) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: Macrophage migration inhibitory factor

B: Macrophage migration inhibitory factor

C: Macrophage migration inhibitory factor

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	67.669, 67.988, 89.135
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Macrophage migration inhibitory factor / MIF / Phenylpyruvate tautomerase / Glycosylation-inhibiting factor / GIF Mass: 13557.404 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MIF / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: P14174, phenylpyruvate tautomerase
#2: Chemical	ChemComp-DHC / CAFFEIC ACID / 3,4-DIHYDROXYCINNAMIC ACID Mass: 180.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₈O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.2 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 30-42.5% MPD_P1K_P3350 mix (MDL Morpheus screen), 0.1M buffer 1 mix (MDL morpheus screen), pH 5.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K PH range: 5.5-7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9702 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2009 / Details: double Si 111 crystal monochromator
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9702 Å / Relative weight: 1
Reflection	Resolution: 1.9→37.3 Å / Num. obs: 32859 / % possible obs: 99.3 % / Redundancy: 4.43 % / B_iso Wilson estimate: 24.8 Å² / R_merge(I) obs: 0.109 / Net I/σ(I): 8.4
Reflection shell	Resolution: 1.9→1.97 Å / Redundancy: 4.53 % / R_merge(I) obs: 0.254 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software

Name	Version	Classification
DNA		data collection
PHASER		phasing
REFMAC	5.5.0088	refinement
CrystalClear		data reduction
CrystalClear		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1CA7

1ca7

Resolution: 1.9→32.27 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.95 / SU B: 5.625 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19958	1663	5.1 %	RANDOM
R_work	0.17283	-	-	-
obs	0.17422	31196	99.3 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 16.023 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.21 Å²	0 Å²	0 Å²
2-	-	-0.59 Å²	0 Å²
3-	-	-	0.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→32.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2662	0	13	272	2947

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	2859
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.408	1.965	3923
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.636	5	389
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.157	24.18	122
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.895	15	460
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.417	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.116	0.2	443
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	2209
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.726	1.5	1805
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.279	2	2930
X-RAY DIFFRACTION	r_scbond_it	2.419	3	1054
X-RAY DIFFRACTION	r_scangle_it	3.835	4.5	971
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.247	117	-
R_work	0.238	2289	-
obs	-	-	99.96 %

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	2.4867	-0.278	-2.1279	1.8678	0.249	4.1423	-0.009	-0.209	0.1748	0.1666	0.0988	0.0687	-0.0764	0.077	-0.0897	0.1018	-0.0029	0.0019	0.1114	0.0164	0.0566	-9.1807	13.2112	-21.9033
2	6.6193	-1.3166	-3.5241	2.8033	0.836	3.8056	-0.0776	-0.1081	0.1222	0.1267	0.0917	-0.0934	0.0107	0.1027	-0.0141	0.0789	-0.0129	-0.04	0.0537	-0.0112	0.0788	1.4587	18.1726	-22.6243
3	10.379	3.6326	-3.5248	3.5996	-1.5314	2.2634	-0.0213	0.2146	0.2344	-0.1616	0.0761	-0.1103	-0.1538	0.0455	-0.0549	0.0952	-0.0049	-0.0081	0.1099	0.0129	0.0702	-1.4871	18.6905	-30.2275
4	3.3588	0.038	0.6683	8.205	1.5948	2.5805	-0.0762	-0.4788	-0.1076	0.7036	0.1671	0.2356	0.0534	-0.1532	-0.0909	0.1261	0.0079	0.0619	0.1724	0.0595	0.0607	-15.4812	4.9069	-16.5017
5	1.7597	-0.602	-0.0711	1.9655	-0.7025	2.4045	0.0349	0.0873	-0.0197	0.0622	-0.0119	-0.1844	0.02	0.1565	-0.023	0.0656	-0.0228	-0.0232	0.0762	0.0036	0.0578	0.3851	6.1263	-28.9003
6	6.956	-2.0888	-4.7955	4.4275	4.5503	7.3391	0.0387	-0.401	-0.027	0.2312	0.0968	-0.3388	-0.2026	0.2643	-0.1355	0.1448	0.0017	-0.0656	0.0759	0.0302	0.0618	2.2401	8.9058	-18.6357
7	4.4586	1.6594	0.6779	3.5031	-0.3021	2.0502	0.0764	-0.4671	-0.2451	0.378	0.0273	-0.0898	-0.0101	0.0415	-0.1038	0.1899	0.0252	-0.0122	0.1446	0.0631	0.0939	-5.5997	3.8749	-14.8129
8	1.6943	-0.3471	0.1061	1.1897	-1.3921	3.8594	0.0319	0.1929	0.0502	-0.0636	0.0052	-0.0215	0.1689	0.1025	-0.0371	0.0161	-0.0138	0.0026	0.1006	0.0168	0.0591	-1.8123	11.2714	-40.5681
9	3.887	0.6412	0.2749	7.052	2.5255	2.5015	0.0325	0.0824	-0.0592	-0.0975	0.0254	0.0916	-0.0752	-0.1842	-0.0579	0.0525	0.0075	-0.0251	0.0961	0.0569	0.0719	-16.2528	16.3761	-36.059
10	1.8717	-0.8388	1.3506	5.2202	4.635	6.7737	-0.0251	0.0663	0.1915	0.0703	-0.039	-0.0371	0.0092	-0.0734	0.0641	0.049	0.0222	0.0182	0.1951	0.0797	0.1653	-24.3419	21.3892	-39.5631
11	3.8654	0.2733	2.0763	0.3622	0.7961	4.9636	0.1429	0.4025	-0.1576	-0.0215	-0.0401	0.0158	0.0683	-0.2431	-0.1029	0.0466	0.0242	0.002	0.1461	0.0432	0.0751	-21.4361	12.0999	-43.9691
12	2.1693	-0.4356	1.3876	4.1595	-0.779	3.9233	0.0761	0.1345	0.5918	0.1301	-0.0666	-0.0626	-0.3126	-0.0395	-0.0095	0.2122	0.0125	-0.0023	0.168	0.0143	0.251	-6.074	24.1811	-29.4759
13	2.2097	0.3541	-0.0353	2.3783	-0.2901	1.6766	-0.0364	0.3831	-0.0716	-0.1254	-0.0356	0.106	0.1946	-0.1669	0.072	0.0588	-0.0221	-0.02	0.1687	0.0163	0.0523	-10.7011	10.4323	-44.6628
14	4.5641	-4.9937	-2.2249	7.7861	4.0501	4.9842	0.0668	0.4412	0.0572	-0.2972	-0.1345	0.2614	-0.2585	-0.1784	0.0677	0.0314	-0.0041	-0.0153	0.1612	0.088	0.0774	-13.3228	20.7071	-46.6844
15	1.7083	0.7126	0.074	3.26	-0.158	1.0605	-0.0134	0.2489	-0.0361	-0.1979	0.0911	-0.0459	0.059	-0.0226	-0.0777	0.0445	-0.0147	-0.0157	0.1197	0.0113	0.036	-11.1912	10.67	-41.0286
16	12.2957	-6.7796	-4.4684	6.6454	2.3898	1.6269	-0.075	0.6322	-0.4886	-0.2091	-0.0947	0.0256	0.0452	-0.2383	0.1697	0.1912	-0.0829	-0.0762	0.2193	-0.0289	0.1974	-23.035	-6.9831	-41.9545
17	6.0202	-3.7578	0.8714	4.7893	0.003	2.9174	-0.0584	-0.1875	-0.2767	0.3152	0.0427	0.3309	0.1051	-0.1188	0.0157	0.0619	-0.0339	0.0297	0.1249	0.079	0.1021	-22.4329	4.5532	-26.4838
18	6.8462	-6.0606	0.2108	9.2357	0.782	3.1787	0.0025	-0.213	-0.5932	0.1352	0.1313	0.4936	0.3669	-0.1411	-0.1338	0.1522	-0.0364	0.0136	0.1421	0.1308	0.1631	-20.8844	-6.3178	-20.9178
19	3.1657	-3.0918	0.9702	5.8687	-4.0853	5.8257	0.0881	-0.2512	-0.0985	0.0196	-0.1135	0.0133	0.3302	0.2571	0.0254	0.1155	-0.0093	-0.024	0.1478	0.0588	0.1193	-14.519	-1.1669	-21.2444
20	4.2322	0.1122	1.3679	2.6923	-0.4295	7.2945	-0.0693	-0.1033	0.0041	0.0027	0.043	0.3659	-0.1323	-0.4035	0.0263	0.0178	0.0126	0.0164	0.1296	0.0792	0.1278	-27.7901	10.756	-34.9528
21	2.6413	0.4222	0.8217	0.5773	-0.1818	0.9531	0.0046	-0.0747	-0.3713	-0.0299	0.1318	0.0012	0.2121	-0.0697	-0.1364	0.1145	-0.0091	-0.0155	0.1104	0.0459	0.142	-15.3764	-3.9086	-32.8873
22	9.1503	-3.2746	-3.9528	4.3039	1.4278	5.0627	-0.0498	0.1301	-0.4361	-0.0954	0.0183	0.1196	0.3495	-0.0126	0.0315	0.1205	-0.0361	-0.0245	0.0986	0.0287	0.1414	-22.3957	-8.807	-32.8253
23	3.2767	-0.2217	-0.0518	3.6936	-3.317	10.255	-0.0225	-0.1817	-0.3519	0.1395	0.1181	0.5551	0.4481	-0.3747	-0.0955	0.085	-0.0242	-0.0043	0.151	0.0427	0.2276	-31.5696	-0.5185	-31.3151
24	3.8282	-0.4919	1.1097	0.9387	-0.2142	0.3338	0.0367	0.0695	-0.2813	0.0357	0.0529	-0.0077	0.0104	-0.0068	-0.0896	0.1074	0.0063	-0.0118	0.0852	0.0405	0.0908	-5.9229	-2.3106	-29.1169

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 12
2	X-RAY DIFFRACTION	2	A	13 - 32
3	X-RAY DIFFRACTION	3	A	33 - 42
4	X-RAY DIFFRACTION	4	A	43 - 54
5	X-RAY DIFFRACTION	5	A	55 - 72
6	X-RAY DIFFRACTION	6	A	73 - 87
7	X-RAY DIFFRACTION	7	A	88 - 95
8	X-RAY DIFFRACTION	8	A	96 - 114
9	X-RAY DIFFRACTION	9	B	1 - 10
10	X-RAY DIFFRACTION	10	B	11 - 23
11	X-RAY DIFFRACTION	11	B	24 - 45
12	X-RAY DIFFRACTION	12	B	46 - 54
13	X-RAY DIFFRACTION	13	B	55 - 72
14	X-RAY DIFFRACTION	14	B	73 - 87
15	X-RAY DIFFRACTION	15	B	88 - 108
16	X-RAY DIFFRACTION	16	B	109 - 114
17	X-RAY DIFFRACTION	17	C	1 - 12
18	X-RAY DIFFRACTION	18	C	13 - 34
19	X-RAY DIFFRACTION	19	C	35 - 42
20	X-RAY DIFFRACTION	20	C	43 - 54
21	X-RAY DIFFRACTION	21	C	55 - 70
22	X-RAY DIFFRACTION	22	C	71 - 84
23	X-RAY DIFFRACTION	23	C	85 - 93
24	X-RAY DIFFRACTION	24	C	94 - 114

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