PDB-4d7k: Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyl...

ID or keywords:

Entry

Database: PDB / ID: 4d7k

Title

Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (RosA) from Streptomyces davawensis

Components

SAM-DEPENDENT METHYLTRANSFERASES

Keywords

TRANSFERASE / METHYLTRANSFERASE / FLAVIN / RIBOFLAVIN / ROSEOFLAVIN BIOSYNTHESIS / ALPHA/BETA TWISTED OPEN-SHEET

Function / homology

Function and homology information

8-amino-8-demethylriboflavin N,N-dimethyltransferase / O-methyltransferase activity / antibiotic biosynthetic process / methylation
Similarity search - Function

Biological species

STREPTOMYCES DAVAWENSIS JCM 4913 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.22 Å

Authors

Uhl, M.K. / Gruber, K.

Citation

Journal: FEBS J. / Year: 2016
Title: Structural and Kinetic Studies on Rosa, the Enzyme Catalysing the Methylation of 8-Demethyl-8-Amino-D-Riboflavin to the Antibiotic Roseoflavin
Authors: Tongsook, C. / Uhl, M.K. / Jankowitsch, F. / Mack, M. / Gruber, K. / Macheroux, P.

History

Deposition	Nov 25, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 2, 2016	Group: Database references
Revision 1.2	Mar 9, 2016	Group: Database references
Revision 1.3	May 4, 2016	Group: Database references
Revision 1.4	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model 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	4d7k.cif.gz	780.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4d7k.ent.gz	655.6 KB	Display	PDB format
PDBx/mmJSON format	4d7k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4d7k_validation.pdf.gz	474.7 KB	Display	wwPDB validaton report
Full document	4d7k_full_validation.pdf.gz	489.1 KB	Display
Data in XML	4d7k_validation.xml.gz	67 KB	Display
Data in CIF	4d7k_validation.cif.gz	92.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d7/4d7k ftp://data.pdbj.org/pub/pdb/validation_reports/d7/4d7k	HTTPS FTP

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Related structure data

Similar structure data	3lst-2 1fp2-1 3gwz-3 3mcz-d 2r3s-d 4x3q-2 3lst-1 2ft3-3 4u1q-1 2wzq-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) 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

Deposited unit

A: SAM-DEPENDENT METHYLTRANSFERASES

B: SAM-DEPENDENT METHYLTRANSFERASES

C: SAM-DEPENDENT METHYLTRANSFERASES

D: SAM-DEPENDENT METHYLTRANSFERASES

E: SAM-DEPENDENT METHYLTRANSFERASES

F: SAM-DEPENDENT METHYLTRANSFERASES

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

1

A: SAM-DEPENDENT METHYLTRANSFERASES

B: SAM-DEPENDENT METHYLTRANSFERASES

defined by author&software
77.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: SAM-DEPENDENT METHYLTRANSFERASES

D: SAM-DEPENDENT METHYLTRANSFERASES

defined by author&software
77.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: SAM-DEPENDENT METHYLTRANSFERASES

F: SAM-DEPENDENT METHYLTRANSFERASES

defined by author&software
77.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.719, 82.760, 96.453
Angle α, β, γ (deg.)	95.08, 98.67, 114.53
Int Tables number	1
Space group name H-M	P1

#1: Protein	SAM-DEPENDENT METHYLTRANSFERASES / N / N-8-AMINO-8-DEMETHYL-D_RIBOFLAVIN DIMETHYLTRANSFERASE Mass: 38808.812 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES DAVAWENSIS JCM 4913 (bacteria) Description: JAPAN COLLECTION OF MICROORGANISMS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 References: UniProt: K4RFM2, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

SAM-DEPENDENT METHYLTRANSFERASES / N / N-8-AMINO-8-DEMETHYL-D_RIBOFLAVIN DIMETHYLTRANSFERASE

Mass: 38808.812 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

STREPTOMYCES DAVAWENSIS JCM 4913 (bacteria)
Description: JAPAN COLLECTION OF MICROORGANISMS / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2
References: UniProt: K4RFM2, Transferases; Transferring one-carbon groups; Methyltransferases

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 269 / 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 % / Description: NONE
Crystal grow	pH: 8 Details: PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 100 MM TRISHCL, PH 5.5 AND 200 MM NACL.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2011 / Details: BENT CYLINDRICAL MIRRORS
Radiation	Monochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.22→34.77 Å / Num. obs: 86780 / % possible obs: 77.4 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / B_iso Wilson estimate: 43.23 Å² / R_merge(I) obs: 0.03 / Net I/σ(I): 12.7
Reflection shell	Resolution: 2.22→2.26 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 1.7 / % possible all: 33

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: MODEL GENERATED WITH MAD

Resolution: 2.22→34.773 Å / SU ML: 0.34 / σ(F): 1.98 / Phase error: 31.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2485	4387	5.1 %
R_work	0.1949	-	-
obs	0.1976	86779	77.43 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.22→34.773 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15510	0	0	269	15779

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	15837
X-RAY DIFFRACTION	f_angle_d	0.618	21505
X-RAY DIFFRACTION	f_dihedral_angle_d	11.027	5731
X-RAY DIFFRACTION	f_chiral_restr	0.025	2409
X-RAY DIFFRACTION	f_plane_restr	0.003	2862

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 (%)
2.22-2.2452	0.3494	83	0.3062	1149	X-RAY DIFFRACTION	32
2.2452-2.2716	0.3467	68	0.2866	1234	X-RAY DIFFRACTION	36
2.2716-2.2993	0.3866	79	0.2775	1391	X-RAY DIFFRACTION	38
2.2993-2.3284	0.3489	83	0.2654	1471	X-RAY DIFFRACTION	42
2.3284-2.3591	0.3487	96	0.2571	1669	X-RAY DIFFRACTION	47
2.3591-2.3914	0.3091	94	0.2601	1737	X-RAY DIFFRACTION	50
2.3914-2.4255	0.3299	83	0.2589	2030	X-RAY DIFFRACTION	56
2.4255-2.4617	0.3285	111	0.2663	2090	X-RAY DIFFRACTION	60
2.4617-2.5002	0.2893	143	0.2678	2410	X-RAY DIFFRACTION	68
2.5002-2.5412	0.3358	143	0.2637	2711	X-RAY DIFFRACTION	76
2.5412-2.585	0.3331	152	0.2616	3301	X-RAY DIFFRACTION	92
2.585-2.632	0.3407	175	0.2503	3392	X-RAY DIFFRACTION	96
2.632-2.6826	0.3288	211	0.2587	3344	X-RAY DIFFRACTION	95
2.6826-2.7373	0.3039	187	0.2502	3359	X-RAY DIFFRACTION	95
2.7373-2.7968	0.3024	188	0.2518	3342	X-RAY DIFFRACTION	95
2.7968-2.8618	0.2948	165	0.2586	3346	X-RAY DIFFRACTION	94
2.8618-2.9333	0.323	166	0.2469	3312	X-RAY DIFFRACTION	93
2.9333-3.0126	0.2907	169	0.2403	3277	X-RAY DIFFRACTION	92
3.0126-3.1012	0.3056	167	0.2342	3276	X-RAY DIFFRACTION	92
3.1012-3.2012	0.2899	182	0.2271	3217	X-RAY DIFFRACTION	91
3.2012-3.3156	0.2847	162	0.2239	3255	X-RAY DIFFRACTION	91
3.3156-3.4482	0.2485	160	0.2131	3206	X-RAY DIFFRACTION	90
3.4482-3.605	0.2801	159	0.2003	3181	X-RAY DIFFRACTION	90
3.605-3.7948	0.2503	164	0.1792	3111	X-RAY DIFFRACTION	88
3.7948-4.0323	0.2273	156	0.1656	3137	X-RAY DIFFRACTION	88
4.0323-4.3431	0.1816	165	0.1482	3151	X-RAY DIFFRACTION	88
4.3431-4.7791	0.2017	180	0.14	3097	X-RAY DIFFRACTION	88
4.7791-5.4684	0.184	177	0.1503	3147	X-RAY DIFFRACTION	89
5.4684-6.8808	0.1969	172	0.1691	3157	X-RAY DIFFRACTION	88
6.8808-34.7776	0.186	147	0.1404	2892	X-RAY DIFFRACTION	82

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	2.5328	-0.621	0.9042	0.7057	-0.8263	2.0568	-0.1017	0.3631	0.2939	0.0731	-0.1017	-0.0426	-0.1082	0.24	0.1749	0.2455	-0.0578	0.0223	0.2056	0.003	0.3787	5.1127	9.3757	-0.338
2	6.7468	-1.6621	-0.3715	5.6326	-1.3788	4.9642	0.0927	1.0042	-0.3892	-0.235	-0.0829	-0.2747	-0.0126	0.0587	-0.0028	0.2568	0.0088	-0.0016	0.6163	-0.1816	0.4474	6.6478	-0.6212	-30.2724
3	7.8727	-4.1812	2.6661	9.0584	-3.0835	8.6971	-0.674	0.8673	1.2251	0.5	0.4798	-0.5264	-1.4848	0.586	0.1158	0.5889	-0.1013	-0.0381	0.9001	0.1861	0.5097	-0.3524	13.0022	-35.2204
4	1.6359	-0.2099	-0.125	2.7995	1.6033	7.0753	0.0371	1.0413	0.2209	-0.3303	-0.0915	0.2004	-0.1518	-0.1754	0.0765	0.1843	0.0138	-0.019	0.7139	0.0554	0.4034	-9.4095	9.4789	-28.3149
5	2.3227	-0.9247	1.168	1.3602	-0.5289	1.5285	-0.2791	0.0419	0.275	0.2591	0.1087	-0.1757	-0.2782	0.0294	0.1539	0.2878	-0.048	0.0126	0.2116	-0.0076	0.4111	-11.5804	20.0788	1.2904
6	8.3695	-2.4336	1.3843	3.8938	-0.1321	5.2907	-0.1951	-0.3758	0.3115	0.6556	0.2216	0.3185	-0.4869	-0.145	-0.026	0.5846	0.1333	0.1432	0.3474	0.1054	0.4885	-21.9187	17.0673	29.9587
7	7.4902	1.9208	1.5816	8.3519	-2.5668	7.0865	-0.2389	-0.4791	1.0915	0.7601	0.0758	-0.4789	-1.0589	0.4765	0.1807	0.7762	0.1905	-0.0968	0.5747	-0.0038	0.3934	-8.69	16.0377	37.2707
8	3.2919	0.3194	-1.7877	2.793	-1.1282	8.7227	-0.2193	-0.5282	-0.1283	0.5815	0.3364	-0.167	0.1024	0.0471	-0.1192	0.3889	0.1397	-0.0051	0.2915	0.049	0.3975	-6.0343	6.5604	29.1945
9	1.994	-0.1264	1.0792	1.8605	-0.4849	3.7321	0.4535	0.0077	-0.2433	-0.0021	-0.003	0.6159	0.8588	0.0651	-0.407	0.4227	0.0125	-0.0995	0.423	-0.1116	0.6208	-44.036	-17.3316	-14.9779
10	7.0498	3.5856	0.1963	6.4078	-0.6922	3.7032	-0.0463	-0.1565	0.3538	0.3827	0.1781	0.4111	-0.2015	-0.2323	-0.1165	0.2275	0.0313	0.0994	0.3121	-0.0299	0.3481	-50.3166	6.6275	5.209
11	8.9253	-4.8132	1.2464	4.9492	-5.1304	8.7314	0.3561	1.0968	0.4711	-0.495	0.554	1.4565	0.4276	-1.2058	-0.7542	0.3178	-0.0789	-0.0621	0.5349	0.1707	0.9246	-50.6868	15.3069	-8.3317
12	4.5287	-0.3604	-0.7329	7.2228	1.6163	4.7995	-0.0363	0.716	0.2593	-0.19	0.1608	0.2625	-0.2481	0.1417	-0.1415	0.1633	-0.0756	0.0331	0.3905	0.0283	0.4519	-39.5819	11.8118	-12.3755
13	1.5871	0.24	-0.1183	2.4349	-1.4908	2.4877	0.099	0.3382	-0.1366	-0.5627	0.1117	0.4166	0.7015	0.3072	-0.1781	0.4346	0.0973	-0.1467	0.529	-0.1706	0.4641	-33.4414	-12.7023	-30.7207
14	8.4574	-0.3315	0.7886	7.2776	-1.9655	4.8475	0.1278	0.3976	-0.3597	-0.6819	0.0311	-0.143	0.4749	0.1607	-0.1723	0.523	0.1281	0.1031	0.5203	0.0754	0.4104	-14.8533	-36.7972	-39.1464
15	9.2396	5.8309	-1.2015	4.7258	2.0822	8.4178	-0.0446	0.5954	-0.7953	0.3431	-0.1228	0.3787	0.5093	-0.8862	0.0314	1.0902	-0.0947	-0.1177	0.66	0.409	0.8972	-23.4011	-48.4647	-33.9864
16	6.0929	-2.938	2.0895	4.2249	0.007	1.0635	-0.6834	-1.5076	-0.9227	0.3581	0.3075	0.4339	0.0415	-0.276	0.3327	0.8142	0.0345	0.0912	0.8165	0.2968	0.7561	-26.5076	-40.9132	-23.1088
17	0.5113	0.6727	-0.0087	2.993	-0.0936	1.8315	0.1413	-0.2463	-0.0522	0.1896	-0.1479	-0.1936	-0.0531	-0.5246	-0.0113	0.4538	0.1331	0.1103	0.5894	0.1514	0.4055	-15.9001	-24.9241	30.9428
18	5.4421	1.1857	2.3934	5.8997	0.4346	2.6799	-0.0691	-2.0956	0.8103	-0.2373	0.0779	0.7411	0.1063	-0.7887	0.0133	0.7223	0.2359	-0.0585	1.4893	-0.2105	0.7626	-47.333	-18.8927	35.5586
19	7.2501	-3.3772	0.3213	7.6754	7.2343	9.6222	-0.3991	0.07	0.1967	-0.7053	-0.0815	0.3591	-1.5717	-1.3763	0.4669	0.6784	0.1261	0.0762	0.7644	0.091	0.4663	-33.9621	-32.2516	19.8416
20	2.003	-8.9067	7.5274	8.5232	-7.8576	8.8558	0.3459	0.498	-2.4056	-1.2768	0.3478	1.9254	1.7028	0.1491	-0.8732	1.151	-0.0407	-0.3439	0.628	-0.0305	0.9218	-46.2212	-36.28	25.4901
21	2.747	-0.5695	-4.5155	8.3053	-0.863	7.9603	-0.5647	1.7583	1.0548	-1.4036	0.5505	0.532	1.1947	-0.4893	-0.0437	0.9557	-0.1614	-0.272	0.7556	0.1718	0.6328	-49.5666	-24.8392	22.3501
22	1.6141	0.0924	0.9584	2.3936	-0.7873	1.8661	0.0058	0.0576	-0.2553	-0.3376	-0.0278	-0.3606	0.2852	-0.1826	0.04	0.5592	0.0929	0.1932	0.4181	0.1093	0.4437	-15.9889	-37.1072	15.3677
23	6.3739	-0.2102	-0.3542	8.5349	1.9987	5.9214	0.0413	0.4065	0.0174	-0.3994	0.0689	-0.3344	-0.158	0.1574	-0.0555	0.3019	-0.0119	0.0925	0.2591	-0.0165	0.3892	7.7799	-30.2022	-4.0034
24	5.5333	-3.2338	2.1889	3.2655	1.715	7.4913	0.2808	-0.3996	-1.1722	0.8328	0.5895	-1.0669	1.3565	0.5027	-0.7421	0.6003	0.0198	-0.247	0.3406	-0.0528	1.2305	16.9048	-28.2271	8.7109
25	7.7049	0.9664	-3.1705	5.1956	-0.8761	6.3771	0.1812	-0.2521	-0.1229	0.8743	0.0643	-0.5009	-0.4454	0.3016	-0.2004	0.3871	0.013	-0.0423	0.2056	-0.0071	0.4958	9.3795	-19.577	12.7383

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 11 THROUGH 165 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 166 THROUGH 246 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 247 THROUGH 272 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 273 THROUGH 345 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 11 THROUGH 165 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 166 THROUGH 240 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 241 THROUGH 272 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 273 THROUGH 345 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 11 THROUGH 173 )
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESID 174 THROUGH 246 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 247 THROUGH 273 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 274 THROUGH 345 )
13	X-RAY DIFFRACTION	13	CHAIN 'D' AND (RESID 10 THROUGH 165 )
14	X-RAY DIFFRACTION	14	CHAIN 'D' AND (RESID 166 THROUGH 246 )
15	X-RAY DIFFRACTION	15	CHAIN 'D' AND (RESID 247 THROUGH 279 )
16	X-RAY DIFFRACTION	16	CHAIN 'D' AND (RESID 280 THROUGH 345 )
17	X-RAY DIFFRACTION	17	CHAIN 'E' AND (RESID 11 THROUGH 165 )
18	X-RAY DIFFRACTION	18	CHAIN 'E' AND (RESID 166 THROUGH 285 )
19	X-RAY DIFFRACTION	19	CHAIN 'E' AND (RESID 286 THROUGH 304 )
20	X-RAY DIFFRACTION	20	CHAIN 'E' AND (RESID 305 THROUGH 323 )
21	X-RAY DIFFRACTION	21	CHAIN 'E' AND (RESID 324 THROUGH 345 )
22	X-RAY DIFFRACTION	22	CHAIN 'F' AND (RESID 11 THROUGH 165 )
23	X-RAY DIFFRACTION	23	CHAIN 'F' AND (RESID 166 THROUGH 246 )
24	X-RAY DIFFRACTION	24	CHAIN 'F' AND (RESID 247 THROUGH 273 )
25	X-RAY DIFFRACTION	25	CHAIN 'F' AND (RESID 274 THROUGH 347 )

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