PDB-8s6q: RosC - Yorodumi

ID or keywords:

Entry

Database: PDB / ID: 8s6q

Title

RosC

Components

Phosphoglycerate mutase

Keywords

HYDROLASE / Streptomyces davaonensis / roseoflavin / riboflavin / phosphatases / antibiotics

Function / homology

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

Function and homology information

Biological species

Streptomyces davaonensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

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

Funding support

1items

Citation

Journal: J.Mol.Biol. / Year: 2024
Title: The Phosphatase RosC from Streptomyces davaonensis is Used for Roseoflavin Biosynthesis and has Evolved to Largely Prevent Dephosphorylation of the Important Cofactor Riboflavin-5'-phosphate.
Authors: Joshi, T. / Demmer, U. / Schneider, C. / Glaser, T. / Warkentin, E. / Ermler, U. / Mack, M.

History

Deposition	Feb 28, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 12, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8s6q.cif.gz	172 KB	Display	PDBx/mmCIF format
PDB format	pdb8s6q.ent.gz	136.3 KB	Display	PDB format
PDBx/mmJSON format	8s6q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8s6q_validation.pdf.gz	4 MB	Display	wwPDB validaton report
Full document	8s6q_full_validation.pdf.gz	4 MB	Display
Data in XML	8s6q_validation.xml.gz	20.9 KB	Display
Data in CIF	8s6q_validation.cif.gz	27.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s6/8s6q ftp://data.pdbj.org/pub/pdb/validation_reports/s6/8s6q	HTTPS FTP

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Related structure data

Related structure data	8s6rC 9emuC C: citing same article (ref.)
Similar structure data	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	#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

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	75.900, 75.900, 162.010
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Phosphoglycerate mutase Mass: 25478.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces davaonensis (bacteria) / Gene: BN159_8033 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K4R812
#2: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 5.7 / Details: PEG 3350, Bis-tris-propane, NaJ

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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: Apr 28, 2019

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. obs: 52968 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.061 / R_rim(I) all: 0.066 / Net I/σ(I): 12.99

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.7-1.8	1.39	8166	0.87	1.501	1
1.8-2	0.532	11909	0.972	0.573	1
2-2.3	0.205	11031	0.993	0.222	1
2.3-2.8	0.095	9527	0.997	0.102	1
2.8-3.4	0.052	5298	0.999	0.057	1
3.4-4.6	0.041	4078	0.998	0.045	1
4.6-5.9	0.037	1501	0.999	0.04	1
5.9-8	0.034	832	0.998	0.037	1
8-12	0.031	419	0.999	0.034	1
12-50	0.029	207	0.998	0.032	1

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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: 1.7→44 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2283	2625	4.98 %
R_work	0.2106	-	-
obs	0.2115	52753	99.64 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.7→44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3053	0	12	115	3180

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017
X-RAY DIFFRACTION	f_angle_d	1.572
X-RAY DIFFRACTION	f_dihedral_angle_d	24.52	450
X-RAY DIFFRACTION	f_chiral_restr	0.093	485
X-RAY DIFFRACTION	f_plane_restr	0.014	556

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 (%)
1.7-1.73	0.3881	134	0.3637	2560	X-RAY DIFFRACTION	98
1.73-1.76	0.3923	151	0.318	2577	X-RAY DIFFRACTION	99
1.76-1.8	0.3092	143	0.2967	2561	X-RAY DIFFRACTION	99
1.8-1.84	0.323	143	0.2874	2553	X-RAY DIFFRACTION	99
1.84-1.88	0.3149	127	0.2905	2629	X-RAY DIFFRACTION	100
1.88-1.93	0.3238	145	0.2717	2577	X-RAY DIFFRACTION	99
1.93-1.98	0.2797	128	0.2453	2606	X-RAY DIFFRACTION	100
1.98-2.04	0.2967	134	0.2275	2625	X-RAY DIFFRACTION	100
2.04-2.11	0.2573	138	0.2132	2614	X-RAY DIFFRACTION	100
2.11-2.18	0.2317	118	0.2101	2618	X-RAY DIFFRACTION	100
2.18-2.27	0.2497	122	0.213	2643	X-RAY DIFFRACTION	100
2.27-2.37	0.2446	132	0.2258	2657	X-RAY DIFFRACTION	100
2.37-2.5	0.2481	160	0.1978	2610	X-RAY DIFFRACTION	100
2.5-2.65	0.2243	134	0.2009	2633	X-RAY DIFFRACTION	100
2.65-2.86	0.2162	146	0.2055	2655	X-RAY DIFFRACTION	100
2.86-3.14	0.2209	133	0.2054	2689	X-RAY DIFFRACTION	100
3.14-3.6	0.2268	164	0.2037	2674	X-RAY DIFFRACTION	100
3.6-4.53	0.1847	123	0.1787	2749	X-RAY DIFFRACTION	100
4.54-44	0.2091	150	0.214	2898	X-RAY DIFFRACTION	100

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	1.0612	1.1866	0.992	5.395	1.0292	0.7778	-0.0424	-0.2374	0.8993	-0.0895	0.0245	1.0703	0.3162	0.1824	0.3204	1.4013	0.0133	0.2212	0.4819	0.0694	0.917	37.2818	28.1053	41.5154
2	4.276	-0.4425	-0.3801	0.1875	0.5525	4.4079	0.0554	0.4548	-1.0379	-0.495	-0.0647	0.0637	0.6841	-0.5072	-0.0428	0.3873	0.0704	-0.0724	0.3342	-0.1024	0.4352	30.8098	-6.1791	36.2503
3	1.9757	-0.0773	-0.4432	2.3353	-0.0055	5.7921	0.0519	0.2322	-0.1335	-0.2044	-0.1059	0.0899	0.079	-0.3743	0.0552	0.2162	0.0507	-0.0053	0.2377	-0.0497	0.2783	36.3886	-2.1423	34.0532
4	4.8757	0.8429	-0.2702	8.3687	-2.1092	3.149	0.1261	-0.6172	0.0263	0.9359	0.1502	0.5805	-0.619	-0.3997	-0.2584	0.2877	0.0587	0.0107	0.294	-0.0042	0.2742	38.6809	2.4373	51.4712
5	4.1825	-1.4049	-0.5165	2.8342	0.3198	3.6397	0.0646	0.0359	0.3391	0.1217	0.0178	0.1406	-0.9002	-0.5568	-0.073	0.3916	0.1189	-0.028	0.2336	0.0134	0.2815	34.5568	8.9816	41.0758
6	8.7224	4.8793	1.3043	7.8638	1.603	6.2482	-0.1391	-0.0721	0.3329	-0.3938	-0.071	0.3007	-1.1108	-0.3305	0.1847	0.4938	0.2166	0.0075	0.3261	0.0253	0.2772	32.3705	12.8207	37.532
7	0.5198	0.1345	0.5096	0.1111	-0.1158	1.0054	0.8691	-0.7949	-1.8031	-0.731	0.4748	0.5191	1.1184	-0.0508	-0.7151	1.5826	0.1015	-0.1998	0.4814	0.0503	1.0646	16.0737	-1.9266	48.0839
8	3.3418	-1.1678	0.4755	0.3663	0.8918	2.9044	0.0782	0.2223	0.6706	-0.3059	-0.15	-0.2723	-0.2715	0.7915	0.0482	0.4073	0.1204	0.0424	0.4901	0.09	0.4057	18.0645	29.5549	33.0122
9	2.6672	-0.9835	-0.0351	3.6084	-0.4328	3.6079	0.2565	0.5605	0.0155	-0.3458	-0.1977	-0.0163	0.3003	0.2566	-0.041	0.2917	0.1597	-0.0216	0.4001	-0	0.2941	12.2003	23.7817	32.0068
10	6.5857	1.4615	2.1224	7.4981	1.5694	5.6102	-0.3331	-0.6554	0.4411	0.944	0.1684	-0.2406	-0.1965	0.2956	0.1287	0.4063	0.1643	-0.0321	0.468	-0.036	0.3394	13.1147	26.1044	51.27
11	4.8537	-1.3878	0.2723	2.4616	-0.4229	3.0379	-0.0122	-0.0028	-0.3047	0.2441	0.1136	-0.1184	0.5784	0.56	-0.0698	0.4403	0.2128	0.0056	0.4037	-0.0128	0.3677	16.8716	16.454	42.7612
12	5.8506	2.0778	-2.2691	5.6048	-3.8351	8.4741	0.0061	-0.1758	-0.2288	-0.294	-0.0978	0.0265	1.1143	0.3784	0.0739	0.5539	0.2192	-0.025	0.3733	0.0053	0.349	18.2898	11.5252	39.9132

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 47 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 48 through 115 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 116 through 148 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 149 through 192 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 193 through 217 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 12 through 26 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 27 through 47 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 48 through 110 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 111 through 148 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 149 through 192 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 193 through 217 )

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