PDB-2yjn: Structure of the glycosyltransferase EryCIII from the erythromyci...

ID or keywords:

Entry

Database: PDB / ID: 2yjn

Title

Structure of the glycosyltransferase EryCIII from the erythromycin biosynthetic pathway, in complex with its activating partner, EryCII

Components

DTDP-4-KETO-6-DEOXY-HEXOSE 3,4-ISOMERASE
GLYCOSYLTRANSFERASE

Keywords

TRANSFERASE / CYTOCHROME P450

Function / homology

Function and homology information

3-alpha-mycarosylerythronolide B desosaminyl transferase / UDP-glycosyltransferase activity / hexosyltransferase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / antibiotic biosynthetic process / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function

Biological species

SACCHAROPOLYSPORA ERYTHRAEA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.091 Å

Authors

Moncrieffe, M.C. / Fernandez, M.J. / Spiteller, D. / Matsumura, H. / Gay, N.J. / Luisi, B.F. / Leadlay, P.F.

Citation

Journal: J.Mol.Biol. / Year: 2012
Title: Structure of the Glycosyltransferase Eryciii in Complex with its Activating P450 Homologue Erycii.
Authors: Moncrieffe, M.C. / Fernandez, M. / Spiteller, D. / Matsumura, H. / Gay, N.J. / Luisi, B.F. / Leadlay, P.F.

History

Deposition	May 20, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 9, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jan 11, 2012	Group: Other
Revision 1.2	Apr 1, 2015	Group: Database references
Revision 1.3	May 8, 2024	Group: Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2yjn.cif.gz	288.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2yjn.ent.gz	238 KB	Display	PDB format
PDBx/mmJSON format	2yjn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2yjn_validation.pdf.gz	442.1 KB	Display	wwPDB validaton report
Full document	2yjn_full_validation.pdf.gz	450.4 KB	Display
Data in XML	2yjn_validation.xml.gz	26.9 KB	Display
Data in CIF	2yjn_validation.cif.gz	37 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yj/2yjn ftp://data.pdbj.org/pub/pdb/validation_reports/yj/2yjn	HTTPS FTP

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Related structure data

Similar structure data	3u30-d 4zpv-d 1irx-d 6urm-d 3i1i-2 1dml-d 3wgv-2 4zpt-d 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	#82 - Oct 2006 Cytochrome p450 similarity (1)

Deposited unit

A: GLYCOSYLTRANSFERASE

B: DTDP-4-KETO-6-DEOXY-HEXOSE 3,4-ISOMERASE

88.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GLYCOSYLTRANSFERASE

B: DTDP-4-KETO-6-DEOXY-HEXOSE 3,4-ISOMERASE

A: GLYCOSYLTRANSFERASE

B: DTDP-4-KETO-6-DEOXY-HEXOSE 3,4-ISOMERASE

defined by author&software
178 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	141.891, 141.891, 141.891
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	195
Space group name H-M	P23

#1: Protein	GLYCOSYLTRANSFERASE / ERYCIII Mass: 48147.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROPOLYSPORA ERYTHRAEA (bacteria) / Strain: NRRL2338 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RP / References: UniProt: O54224, UniProt: A4F7P3*PLUS
#2: Protein	DTDP-4-KETO-6-DEOXY-HEXOSE 3,4-ISOMERASE / ERYCII Mass: 40726.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROPOLYSPORA ERYTHRAEA (bacteria) / Strain: NRRL2338 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RP / References: UniProt: O54225, UniProt: A4F7P2*PLUS

#1: Protein

GLYCOSYLTRANSFERASE / ERYCIII

Mass: 48147.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

SACCHAROPOLYSPORA ERYTHRAEA (bacteria) / Strain: NRRL2338 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RP / References: UniProt: O54224, UniProt: A4F7P3*PLUS

#2: Protein

DTDP-4-KETO-6-DEOXY-HEXOSE 3,4-ISOMERASE / ERYCII

Mass: 40726.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

SACCHAROPOLYSPORA ERYTHRAEA (bacteria) / Strain: NRRL2338 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RP / References: UniProt: O54225, UniProt: A4F7P2*PLUS

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.12 Å³/Da / Density % sol: 60.31 % / Description: NONE
Crystal grow	pH: 8 / Details: 10 MM PHOSPHATE, PH 8, 2MM DTT, 4M SODIUM FORMATE.

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9756 Å / Relative weight: 1
Reflection	Resolution: 3.1→20 Å / Num. obs: 17457 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / B_iso Wilson estimate: 93.73 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 14
Reflection shell	Resolution: 3.1→3.1 Å / Redundancy: 7.5 % / R_merge(I) obs: 0.27 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
autoSHARP		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 3.091→19.677 Å / SU ML: 0.38 / σ(F): 1.33 / Phase error: 27.99 / Stereochemistry target values: ML
Details: CHAIN A RESIDUES 1-18 ARE MISSING CHAIN B RESIDUES 1-19 ARE MISSING

	R_factor	Num. reflection	% reflection
R_free	0.2615	891	5.1 %
R_work	0.2102	-	-
obs	0.2129	17457	98.84 %

Solvent computation

Shrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 74.51 Å² / k_sol: 0.321 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	20.0225 Å²	0 Å²	0 Å²
2-	-	20.0225 Å²	0 Å²
3-	-	-	20.0225 Å²

Refinement step

Cycle: LAST / Resolution: 3.091→19.677 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5419	0	0	0	5419

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	5582
X-RAY DIFFRACTION	f_angle_d	1.862	7659
X-RAY DIFFRACTION	f_dihedral_angle_d	15.451	1929
X-RAY DIFFRACTION	f_chiral_restr	0.082	880
X-RAY DIFFRACTION	f_plane_restr	0.01	1015

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 (%)
3.0912-3.284	0.3245	134	0.2518	2771	X-RAY DIFFRACTION	100
3.284-3.5362	0.3458	154	0.2326	2745	X-RAY DIFFRACTION	100
3.5362-3.8896	0.2969	152	0.2309	2716	X-RAY DIFFRACTION	99
3.8896-4.4468	0.2507	138	0.1916	2746	X-RAY DIFFRACTION	98
4.4468-5.5812	0.2449	156	0.1941	2761	X-RAY DIFFRACTION	99
5.5812-19.6771	0.2376	157	0.2096	2827	X-RAY DIFFRACTION	98

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	3.4413	-0.6631	0.3846	2.7797	0.1726	2.1117	0.1696	-0.0155	0.7451	-0.0087	-0.0179	-0.1549	-0.4905	0.0844	0.0575	0.3428	0.0589	-0.0368	0.1893	0.0252	0.3594	64.9192	-28.9589	-78.2101
2	2.0212	-1.5214	0.1186	1.4947	0.0409	1.0905	-0.0576	-0.123	0.6156	0.1116	-0.0637	-0.2235	-0.3899	-0.0317	-0.0053	0.4563	0.2328	-0.1276	0.2295	-0.0228	0.6154	40.9347	-20.6812	-77.5263
3	0.6273	0.1105	-0.1263	0.567	0.0446	0.3823	0.1206	0.0274	0.3445	-0.1089	-0.0673	0.5634	-0.336	-0.3356	-0.1261	0.1761	0.3467	-0.2541	0.0474	0.2239	0.3712	49.9628	-33.8322	-79.5271
4	5.2469	0.9722	-2.864	0.2725	-0.6314	1.7486	0.2291	-1.2134	-0.2008	0.3298	-0.2019	-0.3433	0.1784	0.4131	0.0601	0.7354	0.202	-0.1168	0.9343	-0.2895	0.7969	60.8863	-26.1127	-44.4865
5	2.9684	-1.1592	0.4537	3.0982	1.3647	4.2818	0.2296	-0.3979	0.3766	0.0004	-0.0391	0.0497	-0.4212	-0.1001	-0.0672	0.4208	0.0409	0.0946	0.4102	-0.0799	0.3764	51.2274	-26.9239	-51.4959
6	1.4911	1.7062	-0.4011	3.1608	-1.5111	3.6289	0.0942	-0.1339	-0.2023	0.2214	-0.139	0.1517	0.3866	0.1404	-0.4042	0.3262	0.0322	-0.0587	0.1813	0.131	0.4413	62.0309	-45.8211	-73.6077
7	0.8024	-0.4397	0.2794	0.6126	-1.0729	2.4199	-0.1225	0.0608	0.0765	0.0038	-0.0878	-0.1957	-0.1689	0.1106	0.0178	1.196	0.4265	0.3287	0.8597	0.1839	1.0534	43.6079	-20.9837	-103.323
8	0.4141	0.3119	0.3515	1.4663	-0.9244	1.4508	0.1146	0.1025	0.1491	-0.1704	-0.0952	0.1283	-0.1377	-0.245	-0.1931	0.5477	0.3804	-0.0954	0.5144	0.0535	0.9275	33.4756	-16.4135	-84.1314
9	2.4225	-0.3059	0.7627	0.8791	0.7773	1.3678	-0.4449	-0.5226	-0.236	0.4092	0.1806	0.3044	0.2516	-0.4349	-0.1006	0.6961	0.2091	0.0233	0.7185	0.0084	1.1044	17.2895	-13.9461	-79.0058
10	0.5079	-0.2628	-0.2561	1.0068	-0.0364	0.4427	-0.0288	0.0356	0.091	-0.1106	-0.0682	0.2238	-0.0766	-0.1574	-0.3063	0.7104	0.5262	-0.2325	0.6166	-0.0897	1.2798	20.0347	-1.0062	-83.2927
11	0.3431	0.2327	-0.1197	0.9083	0.0893	0.6752	-0.0511	-0.0221	0.1571	-0.1434	0.0714	0.0248	-0.223	-0.0867	0.3374	0.598	0.3377	-0.1419	0.3393	0.3836	0.8213	31.5875	-5.3709	-93.8528
12	0.5155	0.4417	0.0674	0.5037	0.2245	0.3009	-0.0946	0.5152	0.0971	-0.0292	0.0424	0.3942	-0.3997	-0.3672	-0.5501	0.6573	0.4001	-0.3267	1.0494	0.1726	1.2154	5.4473	-17.5714	-110.8404
13	1.6888	-0.368	0.6869	1.2351	-0.8739	0.7318	0.2584	-0.6521	-0.5752	0.0064	-0.0478	-0.0214	0.1193	-0.1844	-0.0962	0.5621	0.2926	-0.4245	0.9156	-0.1898	0.6875	11.6716	-23.0028	-107.7172
14	0.5636	-0.0403	0.055	0.6132	0.1563	0.2302	0.0465	0.2177	0.0035	-0.169	-0.0969	0.1204	-0.1292	-0.0606	0.0622	0.5071	0.5243	-0.2179	0.6958	0.1696	0.7662	26.9595	-20.0548	-100.7373
15	0.8216	-0.9	0.1919	1.0289	-0.1635	0.8334	-0.141	0.1606	-0.0523	0.0026	-0.2733	0.0632	0.0908	0.1172	-0.598	0.6001	0.4881	-0.3237	0.7174	-0.1273	1.1438	6.9468	-19.6558	-99.1056
16	1.0039	-1.653	0.6327	2.7848	-0.772	1.5186	-0.1063	0.1777	-0.0357	0.0322	-0.0832	0.1101	0.0381	0.1179	-0.3884	0.4877	0.4228	-0.0641	0.8271	0.0291	1.2241	9.7464	-11.1397	-92.8066
17	1.6394	-1.4326	-0.098	1.2704	-0.0428	0.9329	-0.0045	0.0894	0.2085	0.0612	-0.0603	0.1186	-0.2236	-0.2483	-0.3014	0.4576	0.4386	-0.0209	0.6136	0.022	1.2127	11.5723	-3.8138	-85.2333
18	0.1069	0.0098	0.1156	0.0109	-0.0071	0.1544	-0.0521	0.0914	0.0907	-0.0507	-0.0352	0.1501	-0.1202	-0.1128	-0.8559	0.4274	0.4371	-0.2599	0.721	0.1299	0.9238	5.117	-16.0089	-103.0329
19	1.4937	-1.0912	0.6156	0.7955	-0.4533	0.8205	0.107	-0.0119	-0.3549	-0.0305	0.0447	0.239	0.1156	-0.1197	0.4665	0.4055	0.3401	-0.154	0.4464	0.0959	1.0248	17.1409	-25.5257	-91.5763

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 19:73)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 74:134)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 135:262)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 263:274)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 285:417)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 418:436)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 20:25)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 26:53)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 54:73)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 74:94)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 95:130)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 131:151)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 158:174)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 180:212)
15	X-RAY DIFFRACTION	15	(CHAIN B AND RESID 215:252)
16	X-RAY DIFFRACTION	16	(CHAIN B AND RESID 255:275)
17	X-RAY DIFFRACTION	17	(CHAIN B AND RESID 276:325)
18	X-RAY DIFFRACTION	18	(CHAIN B AND RESID 330:354)
19	X-RAY DIFFRACTION	19	(CHAIN B AND RESID 360:380)

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