PDB-3gac: Structure of mif with HPP

ID or keywords:

Entry

Database: PDB / ID: 3gac

Title

Structure of mif with HPP

Components

Macrophage migration inhibitory factor-like protein

Keywords

CYTOKINE / macrophage migration inhibitory factor

Function / homology

Function and homology information

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

Biological species

Plasmodium yoelii yoelii (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.1 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: 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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PDBx/mmCIF format	3gac.cif.gz	298.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3gac.ent.gz	246.1 KB	Display	PDB format
PDBx/mmJSON format	3gac.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3gac_validation.pdf.gz	499 KB	Display	wwPDB validaton report
Full document	3gac_full_validation.pdf.gz	503.2 KB	Display
Data in XML	3gac_validation.xml.gz	35.7 KB	Display
Data in CIF	3gac_validation.cif.gz	53 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ga/3gac ftp://data.pdbj.org/pub/pdb/validation_reports/ga/3gac	HTTPS FTP

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Related structure data

Related structure data	3gadSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3gad-2 3wnr-d 3gad-1 4gro-3 6lr3-2 3rf4-d 3b9s-d 3hof-d 3rf5-d 3dji-2 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

78.7 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
39.1 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
39.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.500, 99.530, 106.600
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-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.: 3 / Source method: obtained synthetically / Formula: C₂H₄O₂
#4: Chemical	ChemComp-ENO / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / HPP Mass: 180.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₈O₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 788 / 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: 3.26 Å³/Da / Density % sol: 62.25 %
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: 2.1→72.74 Å / Num. obs: 59842 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 26.963 Å² / R_merge(I) obs: 0.064

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
2.1-2.2		0.235	7.9	49995	7587	98.6
2.2-2.3		0.188	10	43291	6429	100
2.3-2.4		0.154	11.9	36311	5426	100
2.4-2.5		0.131	13.9	30845	4569	100
2.5-2.6		0.116	15.4	26398	3929	100
2.6-2.7		0.107	16.6	22686	3369	100
2.7-3		0.077	21.8	51103	7588	100
3-4		0.045	34.8	79930	11934	100
4-5		0.035	43.3	28531	4311	100
5-6		0.041	38.8	12692	1940	100
6-10		0.035	40.4	13653	2122	100
	10	0.028	48.8	3746	638	99.1

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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 3GAD

3gad

Resolution: 2.1→47.75 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.937 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.74 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.421 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19108	1832	3.1 %	RANDOM
R_work	0.15774	-	-	-
obs	0.1588	58009	99.81 %	-

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 mean: 21.275 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→47.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5618	0	55	788	6461

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	5796
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.956	1.962	7876
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.551	5	771
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.431	24.752	282
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.087	15	1022
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.335	15	38
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	860
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	4464
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.188	0.2	2744
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.299	0.2	3948
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.123	0.2	748
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	0.17	0.2	85
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.2	0.2	50
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	0.604	1.5	3747
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.03	2	5838
X-RAY DIFFRACTION	r_scbond_it	1.493	3	2320
X-RAY DIFFRACTION	r_scangle_it	2.313	4.5	2002
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.155 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.224	130	-
R_work	0.157	4137	-
obs	-	-	97.55 %

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	1.9981	0.7505	0.0028	0.3356	0.2876	1.5296	-0.0112	0.0073	0.0013	-0.0104	0.033	0.0305	0.0709	0.0359	-0.0217	-0.0081	0.0035	0.0137	-0.0296	0.0015	-0.0041	2.9023	12.5421	46.7412
2	2.7596	1.2908	-0.6683	1.0838	-0.0136	0.9721	-0.0547	0.0004	-0.003	-0.0842	0.0274	0.0301	-0.0087	0.0748	0.0273	-0.0132	0.0271	-0.0125	-0.0322	0.0186	-0.0445	4.4085	10.9849	52.8083
3	2.5809	0.4648	0.8369	0.428	0.3709	1.1986	0.0062	-0.1404	0.042	0.0491	-0.0251	-0.0017	-0.0118	-0.0555	0.0189	-0.0142	0.0074	0.0131	0.0056	-0.0067	-0.0097	0.7614	14.7386	58.4651
4	6.6427	-1.9768	-4.9425	2.987	5.3324	9.894	0.0975	-0.0634	0.2808	-0.0498	0.0336	-0.16	-0.4415	0.0913	-0.1311	0.0023	-0.0096	-0.0074	-0.0719	0.0366	0.0243	22.6088	4.0452	59.5956
5	0.4611	-0.3246	0.0425	0.4091	0.0361	0.4759	-0.0016	0.025	0.0369	-0.0087	-0.0149	-0.0136	-0.055	0.0009	0.0166	-0.0167	-0.0056	0.0029	-0.0225	0.0027	-0.0095	-5.0344	-5.3748	58.2753
6	0.9587	1.1077	1.6259	1.699	3.2687	7.3685	0.0507	-0.117	-0.0596	0.1349	-0.114	-0.0211	0.2459	-0.365	0.0633	-0.0199	0.0071	0.0135	-0.0247	0.0058	-0.0149	-6.9583	-12.7276	65.0265
7	0.4689	-1.0325	-0.3507	6.4936	3.0015	1.4399	-0.0309	-0.0093	0.0309	-0.0177	0.1347	-0.295	-0.0684	0.0659	-0.1038	-0.0107	-0.0011	0.0017	-0.0038	0.0231	-0.0377	1.8871	-7.78	64.8135
8	2.0693	-2.8372	1.0878	5.9327	-2.9629	6.4441	0.0614	0.0564	0.1436	0.1211	-0.1086	0.0098	0.0508	-0.3336	0.0472	-0.0317	-0.0184	0.0247	0.0449	0.0121	-0.0595	-1.4129	14.7212	66.5948
9	0.7929	-0.0486	0.8056	1.1402	-1.1738	2.2371	-0.0308	0.0869	-0.0539	-0.0418	0.0115	-0.0081	0.0622	0.0404	0.0194	-0.0225	-0.0073	0.0146	-0.0248	-0.0169	-0.012	14.4262	-10.0223	49.1744
10	0.1316	-0.2395	0.1274	3.0978	-1.3165	0.6947	0.0052	0.0107	0.0024	-0.0786	0.0319	0.0978	0.0149	0.0076	-0.0371	-0.0223	-0.0048	0.003	-0.0114	-0.0028	-0.0223	10.8736	-2.0883	49.1303
11	0.4783	-0.0726	0.1301	0.832	-1.2277	3.7292	-0.0173	0.0399	0.0471	0.0559	-0.0083	-0.0187	-0.034	0.0612	0.0256	-0.0308	-0.0106	-0.0093	-0.0446	-0.0087	-0.0101	19.9263	-2.5966	54.0075
12	3.763	-0.4564	-2.1113	1.6684	-0.9128	2.0316	-0.1384	-0.3332	-0.0075	-0.0326	-0.0336	0.1249	-0.1616	0.1465	0.1719	-0.0376	0.0078	-0.008	-0.0078	-0.003	-0.0618	4.9529	-12.2944	70.792
13	1.3832	0.4896	-0.1888	1.1588	-0.0785	0.0259	-0.0509	0.0152	0.0163	0.0056	0.0421	-0.0719	0.0022	-0.014	0.0088	-0.0195	0.0118	-0.0088	-0.014	-0.0016	-0.0127	-17.7001	-26.7967	13.0363
14	3.0275	-0.5543	-0.8489	1.3778	-0.269	1.3453	-0.0825	-0.0412	-0.119	0.0422	0.077	0.0511	0.0532	-0.0382	0.0055	-0.015	-0.0095	-0.0234	-0.0375	0.0001	-0.0525	-26.8521	-25.4313	21.7103
15	2.6043	0.9623	-0.1566	1.3272	-0.1386	0.6062	0.0002	0.049	0.1166	-0.0337	0.0175	0.0139	-0.0049	0.0081	-0.0177	-0.0213	0.0218	-0.0133	-0.0251	0.0067	-0.0215	-22.76	-17.4097	13.4391
16	6.9999	-5.5139	1.4345	11.6953	-4.4521	1.7951	0.0977	0.2062	0.1129	-0.4778	-0.095	-0.2046	-0.0245	0.2001	-0.0027	0.0001	-0.0105	-0.0036	0.0213	-0.0326	-0.0608	-1.6549	-17.2742	24.1291
17	0.145	-0.0341	0.1693	0.339	0.083	0.4716	0.0148	-0.0022	-0.0163	-0.007	0.0027	-0.0002	0.0034	-0.0226	-0.0176	-0.0165	-0.0046	0.0009	-0.0102	0.0005	-0.0152	-29.1097	-19.8778	33.8737
18	1.9686	4.4616	-2.0615	11.9921	-5.4163	3.4981	0.189	-0.1558	0.1738	0.3884	-0.0706	0.3834	-0.2255	-0.0604	-0.1184	-0.0343	0.0149	-0.0008	-0.0041	-0.0137	-0.026	-30.0266	-9.2467	40.0667
19	3.4641	0.7154	-0.0321	1.819	-0.2581	1.1394	0.0391	-0.0723	0.0412	0.1298	0.0045	-0.0063	-0.0637	-0.0054	-0.0436	-0.0243	0.0161	-0.0094	-0.0399	-0.014	-0.027	-26.6892	-19.3126	44.0191
20	1.809	0.1146	1.1536	0.5573	0.0768	10.0892	0.003	0.1617	0.0963	0.0043	-0.0101	0.0159	-0.3181	0.3038	0.0071	-0.0312	0.0321	-0.0025	-0.0747	-0.003	-0.0163	-24.3095	-8.9038	18.729
21	0.3331	0.1949	0.1331	0.303	0.4865	0.9364	0.0038	-0.03	-0.0375	0.0243	-0.0162	0.0151	0.066	-0.0218	0.0124	-0.0027	0.0064	-0.0017	-0.02	0.0095	-0.0061	-10.7146	-26.6984	33.4758
22	1.0508	1.6509	0.9061	11.5057	1.79	1.0758	0.0489	0.0416	-0.1196	0.1409	0.0073	-0.5003	0.0556	0.1448	-0.0562	-0.0434	0.004	0.0082	-0.004	-0.0075	-0.0224	-0.5943	-25.8299	32.6546
23	1.1374	-1.6066	-1.8957	3.8643	3.3351	3.4305	0.1807	0.1036	0.059	-0.4142	-0.0807	-0.0736	-0.2921	-0.0576	-0.1	-0.0203	-0.0146	-0.0122	-0.0166	0.0038	-0.0127	-8.027	-18.7168	28.4399
24	2.8588	0.5799	0.1197	2.8661	-2.5331	2.6037	0.064	-0.1321	0.1178	0.1848	-0.1037	0.0197	-0.0774	-0.1056	0.0397	-0.0089	-0.0001	0.0009	-0.0511	0.0084	-0.0376	-20.6631	-9.112	43.0028

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 25
2	X-RAY DIFFRACTION	2	A	26 - 54
3	X-RAY DIFFRACTION	3	A	55 - 102
4	X-RAY DIFFRACTION	4	A	103 - 116
5	X-RAY DIFFRACTION	5	B	2 - 70
6	X-RAY DIFFRACTION	6	B	71 - 92
7	X-RAY DIFFRACTION	7	B	93 - 105
8	X-RAY DIFFRACTION	8	B	106 - 116
9	X-RAY DIFFRACTION	9	C	2 - 33
10	X-RAY DIFFRACTION	10	C	34 - 56
11	X-RAY DIFFRACTION	11	C	57 - 101
12	X-RAY DIFFRACTION	12	C	102 - 118
13	X-RAY DIFFRACTION	13	D	2 - 37
14	X-RAY DIFFRACTION	14	D	38 - 57
15	X-RAY DIFFRACTION	15	D	58 - 102
16	X-RAY DIFFRACTION	16	D	103 - 116
17	X-RAY DIFFRACTION	17	E	2 - 69
18	X-RAY DIFFRACTION	18	E	70 - 86
19	X-RAY DIFFRACTION	19	E	87 - 99
20	X-RAY DIFFRACTION	20	E	100 - 116
21	X-RAY DIFFRACTION	21	F	2 - 70
22	X-RAY DIFFRACTION	22	F	71 - 92
23	X-RAY DIFFRACTION	23	F	93 - 106
24	X-RAY DIFFRACTION	24	F	107 - 117

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi