PDB-3gad: Structure of apomif

ID or keywords:

Entry

Database: PDB / ID: 3gad

Title

Structure of apomif

Components

Macrophage migration inhibitory factor-like protein

Keywords

CYTOKINE / macrophage migration inhibitory factor

Function / homology

Function and homology information

phenylpyruvate tautomerase / L-dopachrome isomerase / cytokine activity / extracellular space
Similarity search - Function

Biological species

Plasmodium yoelii yoelii (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8 Å

Authors

Zhou, Y.-F. / Su, X.-D. / Shao, D. / Wang, H.

Citation

Journal: Mol.Immunol. / Year: 2010
Title: Structural and functional comparison of MIF ortholog from Plasmodium yoelii with MIF from its rodent host
Authors: Shao, D. / Zhong, X. / Zhou, Y.-F. / Han, Z. / Lin, Y. / Wang, Z. / Bu, L. / Zhang, L. / Su, X.-D. / Wang, H.

History

Deposition	Feb 17, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Dec 29, 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	3gad.cif.gz	171.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3gad.ent.gz	137.1 KB	Display	PDB format
PDBx/mmJSON format	3gad.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3gad_validation.pdf.gz	483.6 KB	Display	wwPDB validaton report
Full document	3gad_full_validation.pdf.gz	487.7 KB	Display
Data in XML	3gad_validation.xml.gz	36.8 KB	Display
Data in CIF	3gad_validation.cif.gz	55.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ga/3gad ftp://data.pdbj.org/pub/pdb/validation_reports/ga/3gad	HTTPS FTP

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Related structure data

Related structure data	3gacC 1mfiS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3gac-2 3b9s-d 3gac-1 1gif-d 4f2k-d 3wns-d 5xej-d 5hvt-d 2oow-d 6cb5-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Macrophage migration inhibitory factor-like protein

B: Macrophage migration inhibitory factor-like protein

C: Macrophage migration inhibitory factor-like protein

D: Macrophage migration inhibitory factor-like protein

E: Macrophage migration inhibitory factor-like protein

F: Macrophage migration inhibitory factor-like protein

hetero molecules

78.6 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Macrophage migration inhibitory factor-like protein

B: Macrophage migration inhibitory factor-like protein

C: Macrophage migration inhibitory factor-like protein

hetero molecules

defined by author&software
39.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Macrophage migration inhibitory factor-like protein

E: Macrophage migration inhibitory factor-like protein

F: Macrophage migration inhibitory factor-like protein

hetero molecules

defined by author&software
39.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	93.880, 98.940, 108.580
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Macrophage migration inhibitory factor-like protein Mass: 12958.597 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium yoelii yoelii (eukaryote) / Gene: mif / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1HEA2
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₄O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 886 / 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: 3.24 Å³/Da / Density % sol: 62.07 %
Crystal grow	Temperature: 289 K / Method: hanging drop / pH: 4.6 Details: 2.5M Ammonium sulfate, 0.1M Sodium acetate trihydrate pH4.6, hanging drop, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site: BSRF

/ Beamline: 3W1A / Wavelength: 1 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 2008

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.8→35.51 Å / Num. obs: 92291 / % possible obs: 98 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 24.511 Å² / R_merge(I) obs: 0.038

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.8-1.9		0.219	7.5	76988	13541	97.3
1.9-2		0.144	12.9	58519	10879	96.2
2-2.1		0.098	17.5	52184	9262	99.7
2.1-2.2		0.069	21.7	44380	7641	99.9
2.2-2.3		0.085	22.2	26457	5590	87.2
2.3-2.4		0.05	28.5	31198	5359	99.9
2.4-2.5		0.045	32	26516	4553	100
2.5-2.6		0.04	35	22918	3929	100
2.6-2.7		0.043	35.1	19005	3319	99.9
2.7-3		0.031	42.8	44186	7588	100
3-4		0.024	60	64165	11711	98.6
4-5		0.019	77.6	24426	4283	99.9
5-6		0.019	73.8	10901	1922	99.9
6-10		0.017	74	11661	2117	99.7
	10	0.014	80.8	2945	597	93.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
MOLREP		phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MFI

1mfi

Resolution: 1.8→34.07 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.935 / WR_factor R_free: 0.194 / WR_factor R_work: 0.16 / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.855 / SU B: 4.432 / SU ML: 0.072 / SU R Cruickshank DPI: 0.103 / SU R_free: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.209	2818	3.1 %	RANDOM
R_work	0.176	-	-	-
obs	0.177	92282	98.01 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 74.89 Å² / B_iso mean: 19.505 Å² / B_iso min: 9.68 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0 Å²	0 Å²
2-	-	0.09 Å²	0 Å²
3-	-	-	-0.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→34.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5389	0	46	886	6321

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	5759
X-RAY DIFFRACTION	r_angle_refined_deg	1.102	1.959	7823
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.2	5	764
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.994	24.764	275
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.859	15	991
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.882	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	858
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4440
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	2757
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	3976
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	836
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.163	0.2	91
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.224	0.2	45
X-RAY DIFFRACTION	r_mcbond_it	0.51	1.5	3745
X-RAY DIFFRACTION	r_mcangle_it	0.804	2	5860
X-RAY DIFFRACTION	r_scbond_it	1.593	3	2261
X-RAY DIFFRACTION	r_scangle_it	2.449	4.5	1942

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.252	213	-
R_work	0.22	6643	-
all	-	6856	-
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	1.4497	0.2953	0.9873	0.6894	0.1405	0.8818	0.0406	0.0263	-0.2008	0.0202	-0.0142	0.0059	0.0483	-0.0537	-0.0264	-0.0228	0	0.004	-0.01	-0.0449	0.0169	-3.0347	-61.5194	-3.7487
2	17.6088	-1.5919	-7.1832	1.2445	1.3119	3.329	0.1988	-0.0302	-0.1898	0.0444	-0.136	0.0633	0.0849	-0.0498	-0.0629	-0.0191	-0.0172	-0.0155	0.0103	0.0028	0.009	-3.852	-59.6019	4.3224
3	3.2579	0.4696	-1.325	1.6451	-0.4175	2.0988	0.0408	-0.1153	-0.5188	0.1831	0.0129	-0.081	0.1612	-0.0796	-0.0537	0.004	-0.0036	-0.0431	-0.0227	0.0185	0.0819	0.2883	-68.5552	3.7383
4	12.4215	-7.3704	-1.2659	4.3856	0.6985	0.3523	-0.0306	-0.48	-0.0803	0.1057	0.1443	0.1029	-0.0037	0.0214	-0.1137	0.055	-0.0399	0.0198	0.0476	-0.0043	0.0546	-12.5368	-57.1472	9.5713
5	13.2418	-7.7523	0.8297	4.6352	-1.8864	20.3486	0.015	-0.0595	-0.7332	0.1139	0.1382	0.5813	1.1972	-0.6204	-0.1532	0.0246	-0.1025	0.0477	-0.0075	-0.0778	0.1081	-24.6008	-53.8224	2.6612
6	0.7531	-0.7415	-0.1728	1.3849	-0.9551	2.3322	-0.0329	-0.0335	-0.0476	0.0558	0.0492	-0.0865	-0.0305	0.1388	-0.0163	-0.0435	-0.0113	-0.0191	-0.0507	0.0038	-0.0277	10.3074	-45.3254	4.3959
7	2.4082	-1.2578	0.4042	1.0697	0.0365	0.7574	0.0214	0.0088	-0.074	0.031	0.0218	0.0754	0.0435	-0.0245	-0.0432	-0.0348	-0.0091	-0.0044	-0.0494	0.0114	-0.061	1.6636	-43.5474	2.2865
8	1.1524	0.1574	-0.0759	1.7466	-0.7569	1.8055	-0.0245	-0.1867	0.0193	0.1572	0.003	-0.0584	-0.0799	0.0701	0.0215	-0.039	0.0124	-0.011	-0.0313	0.0021	-0.0592	4.9071	-39.3116	11.5453
9	0.9047	1.5628	-0.5561	28.8318	-2.7935	4.0601	-0.1484	-0.2714	-0.2289	0.4422	0.4289	0.7733	0.2446	-0.1124	-0.2805	-0.0088	-0.0084	0.0069	0.0196	0.0922	0.0063	-2.2734	-54.6582	16.5105
10	14.8064	-5.5762	-4.4316	9.6228	2.7429	5.397	-0.114	-0.8877	0.2594	0.3858	0.2117	-0.5703	0.123	0.6035	-0.0978	0.0228	0.0026	-0.0603	0.1054	0.0714	-0.0119	1.9768	-65.4001	12.0427
11	1.0027	-0.1398	-0.1066	1.5231	1.2656	1.9509	-0.0168	0.194	0.0962	-0.0791	-0.0163	0.0353	-0.0585	-0.0573	0.0331	-0.0403	0.0097	-0.0201	-0.0162	-0.0074	-0.0374	-13.8024	-39.6534	-4.3455
12	0.8746	-0.2417	-0.2378	3.0121	1.1984	0.5003	0.0281	0.1029	-0.0758	-0.0617	-0.0629	-0.0169	-0.019	-0.0663	0.0348	-0.0298	0.0134	-0.0057	-0.0025	-0.0339	-0.0646	-11.219	-48.3912	-4.51
13	1.1212	-0.5969	0.0568	1.437	1.09	4.1257	-0.0483	0.0317	-0.0361	0.1018	-0.0713	0.1975	-0.033	-0.2279	0.1196	-0.043	-0.008	0.0149	-0.0521	-0.0373	-0.0102	-20.3955	-43.9912	2.0162
14	0.7086	1.5045	2.6075	3.3665	5.3076	10.2948	0.0171	0.0871	-0.2436	0.1874	-0.023	0.1371	0.2327	0.0824	0.0059	-0.0438	-0.0125	0.0174	-0.0118	-0.0614	-0.0044	-19.3529	-52.1373	-1.7191
15	4.1484	0.4948	-0.2126	1.9088	0.4909	1.6607	-0.0588	-0.2822	-0.0516	0.1786	-0.0223	-0.0697	0.0629	0.0786	0.0811	-0.0104	0.0266	-0.0087	0.0008	-0.0121	-0.0495	-4.1532	-37.9393	16.4453
16	1.7451	0.2604	0.3477	1.2129	-0.0993	0.7027	0.0337	0.1741	0.0893	-0.0973	0.0258	0.0727	-0.0205	-0.08	-0.0595	-0.0317	0.0113	0.0118	-0.0028	0.054	-0.0367	19.6211	-22.3747	-40.2435
17	2.5954	-0.2595	0.8468	1.1086	-0.0358	1.582	0.0269	0.0426	0.0638	-0.0141	0.0677	0.0207	0.0227	0.0085	-0.0946	-0.0364	0.0039	0.023	-0.0634	0.0331	-0.0432	24.6254	-25.5403	-33.3642
18	2.5221	0.9977	-0.0247	1.7697	0.2254	1.3503	0.0065	0.2235	-0.1123	-0.1696	0.0242	-0.0673	0.1756	-0.0368	-0.0307	-0.0003	0.0275	0.0022	-0.0192	0.0097	-0.0574	23.4982	-32.4312	-41.1999
19	4.3512	-2.9341	-2.461	3.5994	5.4328	10.1759	-0.0406	0.3635	-0.1394	-0.1457	0.1504	-0.1654	0.0545	-0.4259	-0.1098	0.0081	-0.0592	-0.0083	0.0406	0.0421	0.0035	5.2026	-36.0041	-28.9015
20	9.6772	3.129	1.2625	20.5586	-4.5776	5.6017	0.1739	0.8351	0.1014	-1.1966	-0.1844	0.1018	0.3965	-0.2225	0.0105	-0.0041	-0.0233	-0.028	0.1604	0.0994	-0.0275	-0.251	-29.8898	-30.1453
21	0.7404	0.0786	-0.2752	1.6656	0.2648	0.7074	0.0243	-0.0775	-0.0228	-0.0284	-0.0389	-0.0788	0.0331	0.1759	0.0147	-0.0314	0.004	0.0003	-0.0199	-0.0175	-0.0409	34.3966	-29.384	-19.8577
22	1.5651	-0.4691	-0.505	0.9081	-0.0937	1.1548	0.0842	-0.0055	0.0627	-0.0125	-0.0537	-0.0108	-0.0236	0.0048	-0.0305	-0.0302	-0.0151	0.0138	-0.0732	-0.0178	-0.0475	25.9254	-26.7113	-18.0793
23	1.2876	0.1207	1.2818	3.4774	0.8051	5.2318	-0.0042	-0.0165	-0.1879	-0.1962	-0.0683	0.0782	0.2397	0.0789	0.0726	-0.0126	0.0108	0.0299	-0.0861	-0.0173	-0.0328	25.8783	-41.5692	-22.4408
24	0.7601	0.0808	0.2092	1.576	0.3634	1.6445	0.008	-0.1979	-0.0741	0.1332	-0.004	-0.1008	0.138	0.1407	-0.004	-0.0303	0.0125	0.0041	-0.0255	-0.0054	-0.0417	29.9397	-34.3743	-10.9389
25	0.2617	0.3979	-0.1036	0.6912	0.6289	7.2255	-0.0183	0.0936	-0.0449	-0.0744	-0.0483	-0.0383	0.4055	-0.154	0.0667	0.0222	0.0374	0.0136	-0.0339	-0.0192	-0.0064	25.3017	-41.0408	-34.2872
26	1.3723	0.7534	-0.1352	1.2903	-1.0252	2.487	0.2045	-0.1139	0.2842	0.1601	0.0231	0.1117	-0.3411	-0.0352	-0.2276	0.0088	0.0277	0.0881	-0.06	0.0091	0.0183	11.6195	-18.0594	-17.685
27	0.5017	0.379	-0.6306	0.3179	-0.7172	2.6294	0.0992	0.0293	0.1566	0.0447	0.0519	0.0756	-0.1472	-0.1188	-0.1511	-0.0268	0.019	0.0346	-0.0499	0.0418	0.011	11.0749	-23.4357	-21.6295
28	1.2833	0.3036	-0.7237	5.0166	-1.2772	1.6	0.0233	0.1358	0.1498	0.0098	0.1862	0.3081	0.0293	-0.3618	-0.2095	-0.0424	0	0.0194	0.0039	0.057	-0.0603	3.5513	-27.4934	-20.4058
29	0.1579	-0.6918	0.8116	7.859	-4.8121	4.4978	0.1277	0.3047	0.1384	-0.2365	-0.0381	0	0.2801	-0.1435	-0.0897	-0.0305	-0.0094	0.0076	0.0203	0.0778	-0.0061	5.6254	-26.3056	-28.2399
30	5.6014	0.3226	1.1555	1.2769	0.6441	2.4	0.033	-0.0983	-0.3194	0.0456	0.0363	-0.0156	0.3796	0.1568	-0.0693	0.0425	-0.0024	0.0082	-0.0619	0.0273	-0.0174	20.0346	-42.4375	-12.4057

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 56
2	X-RAY DIFFRACTION	2	A	57 - 67
3	X-RAY DIFFRACTION	3	A	68 - 97
4	X-RAY DIFFRACTION	4	A	98 - 108
5	X-RAY DIFFRACTION	5	A	109 - 116
6	X-RAY DIFFRACTION	6	B	2 - 33
7	X-RAY DIFFRACTION	7	B	34 - 63
8	X-RAY DIFFRACTION	8	B	64 - 99
9	X-RAY DIFFRACTION	9	B	100 - 106
10	X-RAY DIFFRACTION	10	B	107 - 116
11	X-RAY DIFFRACTION	11	C	2 - 33
12	X-RAY DIFFRACTION	12	C	34 - 61
13	X-RAY DIFFRACTION	13	C	62 - 91
14	X-RAY DIFFRACTION	14	C	92 - 101
15	X-RAY DIFFRACTION	15	C	102 - 117
16	X-RAY DIFFRACTION	16	D	2 - 33
17	X-RAY DIFFRACTION	17	D	34 - 63
18	X-RAY DIFFRACTION	18	D	64 - 102
19	X-RAY DIFFRACTION	19	D	103 - 109
20	X-RAY DIFFRACTION	20	D	110 - 116
21	X-RAY DIFFRACTION	21	E	2 - 33
22	X-RAY DIFFRACTION	22	E	34 - 60
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