PDB-8s7m: RosC(R33A) - riboflavin complex

ID or keywords:

Entry

Database: PDB / ID: 8s7m

Title

RosC(R33A) - riboflavin complex

Components

Phosphoglycerate mutase

Keywords

HYDROLASE / Streptomyces davaonensis / roseoflavin / antibiotics / phosphatase

Function / homology

: / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / phosphatase activity / cytoplasm / RIBOFLAVIN / Phosphoglycerate mutase

Function and homology information

Biological species

Streptomyces davaonensis JCM 4913 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Ermler, U. / Mack, M. / Warkentin, E.

Funding support

1items

Citation

Journal: To Be Published
Title: Structural and kinetic analysis of phosphatase RosC, an enzyme of the biosynthesis of antibiotic roseoflavin
Authors: Joshi, T. / Schneider, C. / Glaser, T. / Demmer, U. / Warkentin, E. / Ermler, U. / Mack, M.

History

Deposition	Mar 4, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8s7m.cif.gz	374.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8s7m.ent.gz	305.8 KB	Display	PDB format
PDBx/mmJSON format	8s7m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s7/8s7m ftp://data.pdbj.org/pub/pdb/validation_reports/s7/8s7m	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#257 - May 2021 Fetal Hemoglobin similarity (4) #50 - Feb 2004 Glycolytic Enzymes similarity (4) #225 - Sep 2018 Phytase similarity (1)

Deposited unit

A: Phosphoglycerate mutase

B: Phosphoglycerate mutase

C: Phosphoglycerate mutase

D: Phosphoglycerate mutase

hetero molecules

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

1

A: Phosphoglycerate mutase

B: Phosphoglycerate mutase

hetero molecules

defined by author&software
Evidence: gel filtration
51.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Phosphoglycerate mutase

D: Phosphoglycerate mutase

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.860, 51.990, 81.430
Angle α, β, γ (deg.)	74.19, 81.79, 70.77
Int Tables number	1
Space group name H-M	P1

#1: Protein	Phosphoglycerate mutase / RosC Mass: 25392.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces davaonensis JCM 4913 (bacteria) Gene: BN159_8033 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: K4R812
#2: Chemical	ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 Mass: 376.364 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₀N₄O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.95 Å³/Da / Density % sol: 37.04 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 5 / Details: 25% PEG 1500, 0.1 M TG pH 5.0

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 14, 2020

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.5→50 Å / Num. obs: 108403 / % possible obs: 87.7 % / Redundancy: 3.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.047 / R_rim(I) all: 0.056 / Net I/σ(I): 16.3

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.5-1.6	0.571	11497	0.801	0.68	1
1.6-1.8	0.308	28084	0.943	0.362	1
1.8-2.2	0.1	30944	0.99	0.119	1
2.2-2.8	0.047	19433	0.995	0.057	1
2.8-3.5	0.033	8991	0.996	0.039	1
3.5-4.6	0.029	5285	0.997	0.034	1
4.6-5.9	0.026	2176	0.997	0.032	1
5.9-8	0.023	1184	0.998	0.028	1
8-12	0.021	586	0.999	0.024	1
12-50	0.019	223	0.999	0.023	1

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→48.88 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2082	5493	5.07 %
R_work	0.1779	-	-
obs	0.1795	108358	87.68 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.5→48.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6819	0	114	445	7378

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007
X-RAY DIFFRACTION	f_angle_d	0.908
X-RAY DIFFRACTION	f_dihedral_angle_d	5.768	1045
X-RAY DIFFRACTION	f_chiral_restr	0.082	1106
X-RAY DIFFRACTION	f_plane_restr	0.013	1286

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 (%)
1.5-1.52	0.3039	68	0.282	1644	X-RAY DIFFRACTION	42
1.52-1.53	0.3156	101	0.2694	1790	X-RAY DIFFRACTION	45
1.53-1.55	0.272	94	0.242	1952	X-RAY DIFFRACTION	50
1.55-1.57	0.2593	115	0.2412	2297	X-RAY DIFFRACTION	58
1.57-1.59	0.3115	139	0.2307	2466	X-RAY DIFFRACTION	64
1.59-1.62	0.2786	169	0.2237	2960	X-RAY DIFFRACTION	75
1.62-1.64	0.2507	188	0.2104	3511	X-RAY DIFFRACTION	91
1.64-1.66	0.287	213	0.2036	3684	X-RAY DIFFRACTION	93
1.66-1.69	0.2662	195	0.1973	3671	X-RAY DIFFRACTION	95
1.69-1.72	0.2315	209	0.1976	3745	X-RAY DIFFRACTION	95
1.72-1.75	0.2777	201	0.192	3694	X-RAY DIFFRACTION	95
1.75-1.78	0.2346	174	0.183	3791	X-RAY DIFFRACTION	96
1.78-1.81	0.2446	187	0.1904	3745	X-RAY DIFFRACTION	96
1.81-1.85	0.2218	224	0.1913	3730	X-RAY DIFFRACTION	96
1.85-1.89	0.2376	193	0.1993	3708	X-RAY DIFFRACTION	95
1.89-1.93	0.2694	191	0.1954	3726	X-RAY DIFFRACTION	94
1.93-1.98	0.2437	204	0.1845	3708	X-RAY DIFFRACTION	96
1.98-2.04	0.2042	236	0.1813	3746	X-RAY DIFFRACTION	96
2.04-2.1	0.2151	205	0.1853	3711	X-RAY DIFFRACTION	95
2.1-2.16	0.2378	228	0.1724	3770	X-RAY DIFFRACTION	97
2.16-2.24	0.214	201	0.1756	3752	X-RAY DIFFRACTION	97
2.24-2.33	0.2209	168	0.1796	3786	X-RAY DIFFRACTION	96
2.33-2.44	0.2227	202	0.176	3772	X-RAY DIFFRACTION	97
2.44-2.56	0.2125	175	0.1854	3817	X-RAY DIFFRACTION	97
2.56-2.73	0.1933	189	0.1853	3795	X-RAY DIFFRACTION	96
2.73-2.94	0.2161	206	0.1856	3682	X-RAY DIFFRACTION	96
2.94-3.23	0.1916	209	0.1875	3804	X-RAY DIFFRACTION	97
3.23-3.7	0.1845	228	0.1711	3799	X-RAY DIFFRACTION	97
3.7-4.66	0.1631	203	0.1453	3781	X-RAY DIFFRACTION	97
4.66-48.88	0.1763	178	0.1555	3828	X-RAY DIFFRACTION	97

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	6.0052	-5.3617	0.6534	7.0569	-0.7983	2.0923	0.0727	-0.0776	-0.5861	-0.1276	0.0214	0.5476	0.3352	0.0392	-0.1047	0.202	0.0002	0.013	0.1434	0.0041	0.1932	17.3291	-17.6758	2.5982
2	1.4893	0.519	-0.0689	0.1665	-0.0776	1.6823	-0.0317	-0.0701	-0.3113	-0.0664	0.0716	0.1784	0.3148	-0.0279	-0.0686	0.1539	-0.001	0.0165	0.1254	0.03	0.2762	4.2287	-3.225	-8.1322
3	1.2412	-0.1611	0.0797	2.7823	0.5374	1.2817	0.0216	0.1663	0.2595	-0.0217	0.0098	0.0339	-0.2077	0.0666	-0.0263	0.152	-0.0163	0.0011	0.1585	0.0275	0.2149	6.8545	17.4316	-24.6549
4	0.3237	0.175	0.0057	3.6391	-0.5365	0.4192	0.066	0.0695	0.0154	-0.255	-0.0632	0.2295	0.0508	-0.0522	-0.0027	0.1554	0.0042	-0.0238	0.1452	0.021	0.235	-1.6787	7.3415	-19.8595
5	1.3908	0.2664	0.2222	1.3096	0.2612	1.5316	-0.0355	-0.0402	0.3038	0.1232	0.0382	-0.0137	-0.2735	0.1252	0.018	0.1688	-0.0026	0.001	0.1077	-0.0022	0.2311	5.4746	21.6819	-8.1738
6	5.0163	6.2022	2.7614	2.0653	3.821	3.5813	0.2163	-0.2636	-0.1503	0.3959	-0.2148	0.0743	0.1231	-0.2086	0.0623	0.174	0.0276	-0.0004	0.1496	0.0332	0.2588	-0.048	11.3467	-1.6657
7	0.9733	-0.2517	0.0865	0.6479	0.0137	0.8917	-0.0501	-0.0251	-0.0654	0.0571	0.024	0.0099	0.0169	0.0673	0.0242	0.1302	0.0139	-0.0018	0.1015	0.0042	0.2133	7.0521	6.9437	-7.8941
8	4.2912	2.5024	-0.9141	5.7423	-3.0135	5.3746	0.1356	-0.4077	0.1552	0.3495	0.0693	0.3857	-0.042	-0.355	-0.1416	0.1333	0.0014	0.0188	0.181	0.0003	0.2332	5.2813	-0.5835	-3.6154
9	3.5905	-1.4509	0.0134	2.6545	-1.7379	2.0192	0.17	0.5416	0.4787	-0.2273	-0.2006	-0.2108	-0.8876	0.7746	0.0126	0.2871	-0.05	0.0153	0.2576	0.0668	0.2534	16.2272	7.6681	-23.6116
10	6.9943	-4.9514	1.7333	6.3119	-1.1815	1.5075	0.112	0.0364	0.3643	-0.3724	-0.0796	-0.4097	-0.1686	0.1216	0.0263	0.1912	-0.0418	0.0378	0.1422	-0.001	0.3415	16.3368	26.3938	-16.5929
11	0.8128	-0.2753	0.144	1.3997	-0.1321	1.1517	0.0216	-0.014	-0.0982	-0.0436	-0.0122	-0.1167	0.1134	0.019	-0.0119	0.1257	0.0011	0.0101	0.1216	-0.0059	0.2175	26.0408	-11.2313	-13.7057
12	1.3983	0.2607	-0.6308	1.1456	-0.5308	2.2734	-0.0224	-0.0322	0.1002	0.0706	-0.0165	-0.1941	-0.1316	0.1401	0.017	0.1215	0.007	-0.0132	0.1149	-0.0161	0.2297	29.7455	-2.5845	-6.0651
13	0.986	-0.8149	0.2683	0.7846	-0.0059	2.0835	-0.0109	-0.0874	0.09	0.0656	-0.0069	0.0107	-0.0058	-0.0248	0.0026	0.1162	0.0166	0.0011	0.1337	0.0065	0.224	20.6363	0.1168	-8.5321
14	5.7116	-0.2052	1.0295	3.1892	-0.0014	5.1903	0.0033	0.145	-0.6277	-0.2585	-0.2158	-0.4251	0.1562	0.2239	0.2054	0.3308	0.1176	0.1142	0.2694	0.0542	0.3949	75.9843	-25.6815	14.4083
15	5.2431	-6.4548	0.2306	8.6782	0.192	0.341	-0.035	0.0859	0.248	-0.379	-0.2001	-0.5057	0.1426	0.4871	0.1277	0.2327	0.0397	0.0984	0.2647	0.08	0.2934	57.262	-11.5943	13.0902
16	0.7618	0.3112	0.2814	1.6771	0.0917	1.5643	0.0511	0.0104	0.2606	0.076	0.0214	0.1001	-0.0256	-0.2212	-0.0321	0.1302	-0.0039	-0.0178	0.1371	0.023	0.2074	33.218	7.6987	33.2262
17	8.2579	-2.9645	-3.5052	2.294	1.3504	3.5647	-0.0827	-0.2119	0.0084	0.2013	0.0474	0.0116	0.1488	0.0041	0.0283	0.1134	-0.016	-0.0184	0.0769	-0.0034	0.1488	37.1982	3.5424	42.6735
18	1.4966	-0.0898	0.1932	1.5914	0.2498	1.5138	0.0393	0.0616	-0.0184	-0.1418	-0.0722	0.0874	-0.0096	-0.0707	0.0321	0.0988	0.0177	-0.0036	0.1018	-0.0012	0.1892	36.1731	8.0559	24.6397
19	4.7161	-0.2296	2.8906	6.78	-0.4292	1.7757	0.1367	-0.8009	-0.229	0.8264	-0.0268	0.6296	0.0569	-0.7005	-0.07	0.232	-0.0063	0.0574	0.2925	0.0058	0.2771	35.2431	-4.4886	39.6317
20	3.7035	-2.7644	0.0989	8.3898	0.7742	3.0232	0.0636	-0.3026	-0.5186	0.3199	0.028	0.2045	-0.1091	-0.3184	0.0042	0.0934	-0.0321	0.0055	0.2373	0.0117	0.4073	17.479	1.7046	32.4304
21	1.5351	-0.3014	0.0646	1.5407	0.3813	1.2936	0.018	-0.0529	-0.0769	-0.0226	0.0076	-0.085	0.0683	0.0975	-0.0317	0.1206	0.0056	-0.0057	0.135	0.0247	0.1917	50.0668	-19.8365	29.3919
22	1.8928	0.6971	-0.8596	1.5469	-1.1031	3.066	0.0356	0.2555	-0.0304	-0.2161	-0.029	0.0571	-0.1693	-0.0378	-0.0441	0.1951	0.0155	0.0028	0.1427	-0.0036	0.1845	42.1861	-20.9856	14.3252
23	1.1956	0.1811	0.3518	2.0103	-0.5031	1.4514	0.0112	-0.0048	0.0661	-0.0701	-0.0313	0.1938	-0.0233	-0.0997	-0.0115	0.1413	0.0143	0.008	0.1358	-0.0163	0.247	39.1721	-15.2949	25.5642
24	4.92	1.8495	0.7968	3.1069	0.2259	2.0719	-0.2152	-0.1328	-0.0951	-0.1451	0.0488	-0.1071	-0.0383	0.0145	0.1637	0.1407	0.0258	0.0142	0.1092	-0.0104	0.2425	41.6508	-10.178	29.6613

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 19 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 20 through 33 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 34 through 69 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 70 through 95 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 96 through 131 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 132 through 148 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 149 through 192 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 193 through 207 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 208 through 222 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 19 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 20 through 115 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 116 through 165 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 166 through 222 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid -11 through 4 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 5 through 19 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 20 through 54 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 55 through 68 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 69 through 207 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 208 through 222 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 1 through 19 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 20 through 115 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 116 through 148 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 149 through 192 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 193 through 222 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-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

-
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