PDB-4fx7: Structure of Sym2 D9V+D55V+D130V+D176V

ID or keywords:

Entry

Database: PDB / ID: 4fx7

Title

Structure of Sym2 D9V+D55V+D130V+D176V

Components

Imidazole glycerol phosphate synthase subunit HisF

Keywords

LYASE / FUSION PROTEIN / TIM Barrel / DE NOVO PROTEIN

Function / homology

Function and homology information

imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / L-histidine biosynthetic process / lyase activity / cytoplasm
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.076 Å

Authors

Sterner, R. / Sperl, J.M. / Rajendran, C.

Citation

Journal: To be Published
Title: Structure of Sym2 D9V+D55V+D130V+D176V
Authors: Sterner, R. / Sperl, J.M. / Rajendran, C.

History

Deposition	Jul 2, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 2, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jun 7, 2017	Group: Database references / Structure summary
Revision 1.2	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	4fx7.cif.gz	368.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4fx7.ent.gz	304.7 KB	Display	PDB format
PDBx/mmJSON format	4fx7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4fx7_validation.pdf.gz	465.1 KB	Display	wwPDB validaton report
Full document	4fx7_full_validation.pdf.gz	470 KB	Display
Data in XML	4fx7_validation.xml.gz	36.9 KB	Display
Data in CIF	4fx7_validation.cif.gz	52 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fx/4fx7 ftp://data.pdbj.org/pub/pdb/validation_reports/fx/4fx7	HTTPS FTP

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Related structure data

Similar structure data	3tdm-1 5l6u-d 3tdn-1 5ahi-d 3tdn-2 6uvz-5 5ac8-d 5g5i-d 5g2h-d 5g2w-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) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Imidazole glycerol phosphate synthase subunit HisF

B: Imidazole glycerol phosphate synthase subunit HisF

C: Imidazole glycerol phosphate synthase subunit HisF

D: Imidazole glycerol phosphate synthase subunit HisF

hetero molecules

110 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Imidazole glycerol phosphate synthase subunit HisF

hetero molecules

defined by author&software
27.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Imidazole glycerol phosphate synthase subunit HisF

hetero molecules

defined by author&software
27.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Imidazole glycerol phosphate synthase subunit HisF

hetero molecules

defined by author&software
27.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Imidazole glycerol phosphate synthase subunit HisF

hetero molecules

defined by author&software
27.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.616, 83.265, 80.154
Angle α, β, γ (deg.)	90.00, 102.66, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Imidazole glycerol phosphate synthase subunit HisF / IGP synthase cyclase subunit / IGP synthase subunit HisF / ImGP synthase subunit HisF / IGPS subunit HisF Mass: 27252.422 Da / Num. of mol.: 4 / Mutation: A3R, D9V, Y22H, D55V, D130V, Y143H, D176V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: hisF, TM_1036 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): T7 References: UniProt: Q9X0C6, Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Chemical	ChemComp-PI / HYDROGENPHOSPHATE ION Mass: 95.979 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: HO₄P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.18 %

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Data collection

Diffraction

ID	Crystal-ID
1	1
2	1

Diffraction source

Source	Site	Beamline	ID
SYNCHROTRON	SLS	X06DA	1
SYNCHROTRON	ESRF	ID14-4	2

Radiation

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

Radiation wavelength

Relative weight: 1

Reflection

Resolution: 2.076→46.72 Å / Num. obs: 49448 / Observed criterion σ(F): 3.5 / Observed criterion σ(I): 1.8

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.076→46.716 Å / SU ML: 0.27 / σ(F): 2 / σ(I): 1.8 / Phase error: 22.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2329	2474	5 %	RANDOM
R_work	0.1717	-	-	-
all	0.23	92390	-	-
obs	0.1747	49445	95.64 %	-

Solvent computation

Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.347 Å² / k_sol: 0.356 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.4035 Å²	-0 Å²	0.0188 Å²
2-	-	-0.461 Å²	-0 Å²
3-	-	-	0.0575 Å²

Refinement step

Cycle: LAST / Resolution: 2.076→46.716 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7189	0	40	348	7577

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7331
X-RAY DIFFRACTION	f_angle_d	1.086	9932
X-RAY DIFFRACTION	f_dihedral_angle_d	12.441	2616
X-RAY DIFFRACTION	f_chiral_restr	0.069	1200
X-RAY DIFFRACTION	f_plane_restr	0.004	1255

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 (%)
2.0763-2.1163	0.3699	87	0.2887	1638	X-RAY DIFFRACTION	61
2.1163-2.1595	0.3108	136	0.2512	2593	X-RAY DIFFRACTION	96
2.1595-2.2064	0.2856	136	0.2262	2589	X-RAY DIFFRACTION	96
2.2064-2.2578	0.2923	138	0.2188	2611	X-RAY DIFFRACTION	95
2.2578-2.3142	0.2915	138	0.2121	2627	X-RAY DIFFRACTION	96
2.3142-2.3768	0.2703	138	0.2049	2613	X-RAY DIFFRACTION	97
2.3768-2.4467	0.2626	139	0.1899	2640	X-RAY DIFFRACTION	97
2.4467-2.5257	0.3056	140	0.1857	2667	X-RAY DIFFRACTION	99
2.5257-2.616	0.2672	142	0.178	2691	X-RAY DIFFRACTION	99
2.616-2.7207	0.2604	142	0.1662	2698	X-RAY DIFFRACTION	99
2.7207-2.8445	0.2008	142	0.1566	2700	X-RAY DIFFRACTION	99
2.8445-2.9944	0.2016	142	0.1545	2698	X-RAY DIFFRACTION	99
2.9944-3.182	0.2346	144	0.1548	2736	X-RAY DIFFRACTION	99
3.182-3.4276	0.2398	141	0.1604	2684	X-RAY DIFFRACTION	99
3.4276-3.7724	0.1861	144	0.1546	2723	X-RAY DIFFRACTION	99
3.7724-4.318	0.1995	140	0.1417	2670	X-RAY DIFFRACTION	98
4.318-5.4389	0.1747	142	0.144	2692	X-RAY DIFFRACTION	97
5.4389-46.7278	0.2263	143	0.1839	2701	X-RAY DIFFRACTION	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	0.2171	-0.0517	0.1413	0.0249	-0.0149	0.1064	0.1126	-0.0363	-0.2157	0.0308	-0.0998	0.0597	-0.0432	0.1073	-0.0041	0.1119	-0.0107	0.0076	0.1089	0.031	0.1727	-4.9168	5.8469	112.2038
2	0.0329	-0.0215	0.0257	0.0722	-0.0231	0.0942	0.0333	-0.0406	0.0159	0.0969	0.0237	-0.1514	0.0756	-0.0354	0.0001	0.16	0.0088	-0.0054	0.1133	-0.0083	0.1495	3.396	5.3039	111.0299
3	0.3478	0.1781	-0.0205	0.1444	-0.0533	0.0465	0.0983	-0.2133	-0.203	0.0307	-0.0235	-0.0827	-0.0375	0.0233	0.0197	0.1127	0.0369	0.0303	0.114	-0.0193	0.0542	5.1071	15.256	121.1365
4	0.0718	-0.0486	0.0013	0.0301	0.0012	-0.0007	0.0151	-0.0478	0.0374	0.0787	-0.0104	-0.0595	0.0054	0.0218	-0.0906	0.1225	-0.1088	-0.1445	-0.1414	-0.2385	0.1616	10.8353	28.2776	121.9428
5	0.2535	-0.033	0.0604	0.0871	0.0778	0.1072	0.0711	0.1228	0.0223	0.0166	-0.0658	0.0822	-0.0433	0.0274	0.0008	0.0767	0.0039	-0.013	0.0696	0.0073	0.163	-4.9126	28.4535	110.456
6	0.0606	-0.0439	-0.0232	0.0335	0.022	0.1504	-0.0243	0.0705	0.041	-0.1784	0.0321	-0.1262	-0.2101	-0.0146	0.0048	0.1485	-0.0006	0.0254	0.0963	-0.04	0.1469	2.1018	29.5368	108.8317
7	0.2882	-0.1903	-0.0031	0.2232	0.0383	0.0129	0.1503	0.2645	0.0836	-0.1912	-0.0976	-0.044	-0.1664	0.0335	0.0226	0.1888	-0.039	0.0375	0.1289	-0.002	0.0926	1.4264	22.0709	97.7504
8	0.1579	0.1037	-0.1046	0.3395	-0.031	0.0846	0.0089	0.0356	0.119	-0.2786	0.0249	0.0186	-0.0025	0.0691	0.0124	0.165	0.01	0.0404	0.1296	-0.0189	0.0917	4.2639	9.5739	98.7965
9	0.0691	-0.0288	-0.1918	0.1267	0.0205	0.5821	0.0187	-0.0617	-0.0551	-0.1064	0.0225	-0.0225	-0.1026	0.1468	0.0645	0.0808	-0.0448	0.0147	0.0471	0.0158	0.2519	11.794	32.0249	75.6028
10	0.1155	-0.0073	-0.0611	0.0438	-0.0324	0.2482	0.1509	-0.0105	0.1039	-0.0764	-0.0056	-0.1384	-0.3162	0.0689	0.008	0.2011	0.0027	-0.0151	0.1332	0.0316	0.2711	16.7876	38.7341	76.4163
11	0.1914	0.2283	-0.034	0.2543	-0.027	0.1808	0.1029	-0.084	-0.037	0.1397	-0.1029	-0.2736	0.0097	-0.0196	0.0009	0.1441	0.0065	-0.023	0.1006	0.0164	0.1488	14.9626	22.8941	81.653
12	0.0535	-0.0153	0.0237	0.1972	0.234	0.3121	-0.1805	-0.1132	-0.0773	0.1374	-0.0753	0.0394	0.0421	0.0683	-0.0421	0.2122	0.0331	0.0053	0.1282	0.0222	0.1954	9.4757	8.586	81.546
13	0.1536	-0.0234	-0.0334	0.0026	0.0409	0.515	0.0022	0.2131	-0.0851	-0.1094	0.1309	0.045	-0.0325	0.0677	0.0922	0.2145	-0.0176	0.029	0.1424	-0.0251	0.0938	11.0579	17.3446	68.1154
14	0.3284	-0.1928	-0.1008	0.3037	0.1695	0.2705	0.0502	0.1268	-0.1352	-0.1241	-0.108	-0.0044	-0.0075	-0.0235	-0.2127	0.1409	0.0691	0.2399	0.1045	-0.1177	0.1052	19.4509	14.4388	61.1916
15	0.5411	-0.1184	0.2247	0.0271	-0.0468	0.098	0.0931	0.1097	-0.3123	-0.0711	0.1166	-0.0048	-0.0423	0.0581	0.075	0.1911	0.0043	0.0658	0.1119	-0.0496	0.1797	9.2379	14.2894	66.2923
16	0.7899	0.2315	-0.2886	0.3993	-0.0719	0.1487	-0.1829	0.5083	0.0934	-0.2402	0.1234	0.0894	-0.1379	-0.2085	0.0105	0.1874	0.0142	-0.0377	0.1121	0.1103	0.1256	3.9633	29.0586	63.6522
17	0.0595	-0.1295	-0.1127	0.2828	0.27	0.262	0.2189	-0.0653	-0.1063	-0.0911	-0.0023	-0.0529	-0.1383	-0.3769	0.1451	0.0337	0.0186	-0.0128	0.3009	0.07	0.1847	27.5946	28.3083	103.5463
18	0.0383	-0.0907	-0.0769	0.2207	0.2013	0.191	-0.0809	-0.0931	0.1254	-0.1522	-0.0698	-0.0583	-0.3795	-0.2598	-0.033	0.2137	0.0547	0.042	0.266	-0.0074	0.1968	31.4247	35.4791	101.9393
19	0.1292	-0.0784	-0.0066	0.1687	0.0649	0.1116	0.1228	0.0162	-0.0214	-0.0726	-0.09	0.0832	-0.0851	-0.0977	0.0002	0.139	-0.0099	-0.0253	0.1548	0.0176	0.1467	31.2493	18.4597	95.1204
20	0.1189	0.0634	0.0546	0.194	-0.1607	0.2512	-0.0445	-0.1086	0.091	-0.0277	-0.1735	-0.015	0.1061	-0.1189	-0.0209	0.2275	0.0248	-0.0514	0.1276	-0.0478	0.1802	38.7811	5.2451	93.1908
21	0.0255	-0.0315	-0.0009	0.1294	0.0061	0.0008	0.0673	-0.0006	-0.1554	0.135	-0.0448	0.195	-0.032	-0.0582	-0.002	0.1483	-0.0295	0.0145	0.2261	0.0141	0.1698	36.2726	11.8443	107.9899
22	0.0881	0.0999	0.1103	0.2586	0.1954	0.1772	0.1533	0.0117	0.002	0.1205	0.0544	-0.0931	0.0017	0.0108	0.0404	0.1678	-0.0206	0.0299	0.1819	0.0586	0.1438	34.4539	7.7233	111.3529
23	0.3188	0.1708	0.1538	0.1657	-0.0527	0.2338	0.0573	-0.213	0.0096	0.1237	-0.1083	-0.0432	-0.0498	-0.0986	-0.0001	0.1258	0.0029	0.0066	0.1824	-0.0045	0.1392	41.7631	23.4702	113.6075
24	0.021	-0.0547	0.0324	0.2348	-0.1252	0.0739	0.1871	0.2989	-0.1135	0.0735	-0.2068	-0.2542	0.0669	-0.0586	-0.0172	0.1652	-0.0148	0.017	0.2307	-0.063	0.1665	53.4234	8.8135	62.7885
25	0.4812	-0.2232	-0.0332	0.1742	0.1356	0.3865	0.0603	0.3345	-0.2047	-0.1489	-0.069	0.0575	0.1057	-0.0128	-0.0041	0.1838	-0.0295	-0.0543	0.2852	-0.016	0.1518	43.1683	14.528	57.4598
26	0.0981	-0.0206	-0.0636	0.2411	0.0534	0.2038	0.0228	0.086	0.3392	-0.0927	-0.1141	0.1167	-0.0762	0.0419	0.0001	0.2353	-0.0112	-0.0698	0.3224	0.0305	0.3019	45.0338	30.7058	65.6006
27	0.1126	0.0736	-0.041	0.1432	0.1005	0.1506	0.1227	-0.1973	0.0656	0.1668	-0.1563	0.0807	0.0769	-0.2372	-0.0001	0.1844	-0.0165	0.0034	0.2923	-0.0085	0.1689	44.6875	17.654	77.7726

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:31)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 32:54)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 55:109)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 110:121)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 122:152)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 153:175)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 176:216)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 217:241)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 1:13)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 14:42)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 43:109)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 110:121)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 122:134)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 135:152)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 153:175)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 176:241)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 1:25)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 26:42)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 43:109)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 110:121)
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 122:134)
22	X-RAY DIFFRACTION	22	chain 'C' and (resseq 135:175)
23	X-RAY DIFFRACTION	23	chain 'C' and (resseq 176:240)
24	X-RAY DIFFRACTION	24	chain 'D' and (resseq 2:31)
25	X-RAY DIFFRACTION	25	chain 'D' and (resseq 32:109)
26	X-RAY DIFFRACTION	26	chain 'D' and (resseq 110:175)
27	X-RAY DIFFRACTION	27	chain 'D' and (resseq 176:240)

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-Yorodumi

-
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

-
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

-
Yorodumi