PDB-8s6r: RosC-8.demethyl-8-amino-riboflavin complex

ID or keywords:

Entry

Database: PDB / ID: 8s6r

Title

RosC-8.demethyl-8-amino-riboflavin complex

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 / Chem-RS3 / Phosphoglycerate mutase

Function and homology information

Biological species

Streptomyces davaonensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.25 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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Download

PDBx/mmCIF format	8s6r.cif.gz	194.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8s6r.ent.gz	153.3 KB	Display	PDB format
PDBx/mmJSON format	8s6r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s6/8s6r ftp://data.pdbj.org/pub/pdb/validation_reports/s6/8s6r	HTTPS FTP

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Related structure data

Related structure data	8s6qC 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

51.9 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)	58.780, 81.420, 89.350
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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-Gold(DE3)pLysS AG' (bacteria) References: UniProt: K4R812
#2: Chemical	ChemComp-RS3 / 1-deoxy-1-[8-(dimethylamino)-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl]-D-ribitol / Roseoflavin Mass: 405.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₂₃N₅O₆ / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.1 Å³/Da / Density % sol: 41.37 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 5 / Details: PEG 1500, TGB

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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: Feb 2, 2021

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.25→50 Å / Num. obs: 117944 / % possible obs: 99.1 % / Redundancy: 11.2 % / CC_1/2: 1 / R_merge(I) obs: 0.052 / R_rim(I) all: 0.054 / Net I/σ(I): 19.7

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.25-1.3	1.541	12023	0.474	1.732	1
1.3-1.4	2.972	20864	0.629	3.139	1
1.4-1.6	0.741	27742	0.958	0.78	1
1.6-1.9	0.16	22787	0.996	0.168	1
1.9-2.4	0.072	17136	0.999	0.074	1
2.4-3	0.047	8333	0.999	0.049	1
3-3.8	0.038	4501	0.999	0.04	1
3.8-4.6	0.033	1932	1	0.034	1
4.6-5.9	0.032	1345	0.999	0.033	1
5.9-8	0.034	737	1	0.035	1
8-12	0.028	375	1	0.029	1
12-50	0.029	169	1	0.03	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: 1.25→32.59 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2085	2000	1.7 %
R_work	0.1891	-	-
obs	0.1895	117823	99.35 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.25→32.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3360	0	60	311	3731

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011
X-RAY DIFFRACTION	f_angle_d	1.187
X-RAY DIFFRACTION	f_dihedral_angle_d	11.756	1343
X-RAY DIFFRACTION	f_chiral_restr	0.099	556
X-RAY DIFFRACTION	f_plane_restr	0.013	647

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 (%)
1.25-1.28	0.3554	131	0.3634	7636	X-RAY DIFFRACTION	93
1.28-1.32	0.3528	141	0.3426	8136	X-RAY DIFFRACTION	99
1.32-1.36	0.3596	142	0.3269	8239	X-RAY DIFFRACTION	100
1.36-1.4	0.3613	142	0.3488	8223	X-RAY DIFFRACTION	100
1.4-1.45	0.3299	142	0.306	8209	X-RAY DIFFRACTION	100
1.45-1.51	0.2902	145	0.2569	8325	X-RAY DIFFRACTION	100
1.51-1.58	0.244	142	0.2283	8229	X-RAY DIFFRACTION	100
1.58-1.66	0.2708	143	0.2146	8275	X-RAY DIFFRACTION	100
1.66-1.76	0.2343	143	0.2186	8300	X-RAY DIFFRACTION	100
1.76-1.9	0.2352	144	0.1867	8338	X-RAY DIFFRACTION	100
1.9-2.09	0.1888	144	0.1721	8348	X-RAY DIFFRACTION	100
2.09-2.39	0.2206	144	0.1735	8376	X-RAY DIFFRACTION	100
2.39-3.01	0.1864	146	0.1821	8447	X-RAY DIFFRACTION	100
3.01-32.59	0.1728	151	0.1623	8742	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	3.4066	5.3451	-0.251	8.4445	0.2836	8.6871	0.0279	-0.5474	-0.0659	0.4069	0.0059	-0.7863	-0.1986	0.6356	-0.1008	0.3327	0.033	-0.063	0.233	-0.0764	0.3193	33.2548	12.3315	-6.3604
2	4.887	2.8158	-0.7326	3.3733	-1.0065	1.2785	0.1975	-0.6241	0.339	0.3937	-0.1956	0.2016	-0.1284	0.1099	-0.0046	0.2461	0.0605	0.0255	0.2845	-0.0203	0.1583	13.7159	3.2306	-1.1391
3	8.4222	-4.6767	1.7674	2.6731	-1.742	6.9377	0.2184	0.2695	-1.0818	-0.4483	-0.005	0.6357	0.6741	-0.247	-0.156	0.2735	-0.0225	0.002	0.2382	0.0313	0.4094	-7.7955	-14.7941	-11.7531
4	1.7816	-0.9193	0.4093	1.6449	-0.9712	2.1017	-0.1543	-0.3281	-0.1349	0.2638	0.1711	0.1661	-0.001	-0.1878	-0.0175	0.1996	0.0384	0.0567	0.271	0.0578	0.2226	0.7746	-7.2404	-1.1413
5	1.7135	0.441	-1.5307	2.7974	0.4006	2.6613	-0.1636	0.2681	-0.0227	-0.1903	0.0859	0.3369	0.0283	-0.325	0.0885	0.1819	0.0017	-0.0313	0.2875	0.0626	0.2494	-5.7071	-0.2961	-23.7861
6	8.3164	-1.0019	5.4746	1.3958	-1.1702	3.8191	-0.3167	-0.4145	0.4819	0.1523	0.1349	-0.057	-0.6517	-0.4363	0.1723	0.2468	0.0624	0.0131	0.1908	-0.0226	0.2722	0.6514	9.0915	-7.2641
7	2.1132	-0.2691	-0.2133	1.4416	-0.7626	1.6912	-0.1258	-0.3004	0.0949	0.1749	0.117	0.004	-0.1362	0.0058	0.008	0.1637	0.0465	0.0075	0.2013	0.013	0.1662	8.0152	1.8158	-8.4279
8	4.9448	0.543	-0.1815	6.9592	-0.3958	4.1029	-0.043	-0.2239	-0.1044	0.0536	-0.0068	0.2244	0.0047	-0.1592	0.0777	0.0945	0.0394	0.0066	0.209	0.0328	0.0989	12.6024	-3.5073	-6.7656
9	2.7863	3.8191	-1.7948	6.5229	-0.2948	5.7037	0.0166	0.51	-0.4662	-0.0369	0.1394	0.3242	0.2081	-0.425	-0.1228	0.2209	-0.0059	0.0104	0.213	-0.0194	0.3148	-3.1133	-11.5161	-23.2821
10	1.3085	-0.5087	1.7361	4.9128	2.4665	5.3395	0.1937	0.0006	-0.5306	0.003	-0.1059	0.3238	0.311	-0.3332	-0.1168	0.1578	-0.0072	0.0244	0.1695	0.0042	0.2274	18.3732	-13.0953	-18.0443
11	5.1661	0.5666	-0.8905	7.9468	-2.4514	4.4898	-0.0356	-0.8914	0.8395	0.7643	-0.0899	-0.7722	-0.6056	0.9016	0.1188	0.2594	-0.0258	-0.0674	0.3839	-0.0924	0.3471	40.1965	1.6682	-3.7879
12	1.8059	0.3516	-0.3593	1.6519	0.1906	1.638	-0.0616	-0.2541	-0.164	0.2069	0.043	-0.2038	0.102	0.1027	0.0196	0.1931	0.037	-0.0166	0.213	0.0456	0.2149	31.4448	-11.6963	-6.2088
13	2.7184	1.5203	-1.8973	6.65	-2.7894	2.8811	-0.0006	-0.0679	0.1226	-0.1213	-0.019	-0.4156	-0.025	0.0917	0.0252	0.1142	0.0117	-0.0096	0.165	0.0028	0.1983	36.8865	-3.2192	-17.5088
14	1.4947	-2.4393	0.6238	6.8305	2.5534	5.4114	-0.0341	-0.0448	0.2832	-0.0138	0.1121	-0.3504	-0.1854	0.127	-0.0571	0.212	-0.0228	0.0338	0.1216	0.0152	0.2422	31.184	13.8014	-18.5527
15	2.3328	1.3959	-0.2855	3.0884	-3.0817	3.8158	-0.0861	0.1306	0.0614	-0.7701	0.0098	-0.2445	0.0222	-0.1774	0.0737	0.2197	0.0202	0.0077	0.1657	-0.0111	0.1447	28.5935	-4.8075	-26.0808
16	1.6063	0.5867	1.3858	8.5163	4.8143	3.6023	-0.0065	-0.1093	-0.2395	0.0184	-0.1612	0.2445	0.252	-0.1409	0.1715	0.1527	0.0123	0.0333	0.126	0.0272	0.1785	24.7898	-18.0531	-16.7826
17	1.6776	0.1554	0.383	1.1687	-0.5348	1.3062	-0.0538	-0.0289	0.0017	-0.0635	0.0355	-0.0207	-0.0605	-0.0425	0.0154	0.174	0.0131	0.0102	0.1728	-0.0002	0.1732	21.0052	-2.4274	-14.477

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 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 54 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 55 through 110 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 111 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 222 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 2 through 19 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 20 through 33 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 34 through 54 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 55 through 94 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 95 through 115 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 116 through 131 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 132 through 148 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 149 through 165 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 166 through 222 )

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