PDB-5w4z: Crystal Structure of Riboflavin Lyase (RcaE) with modified FMN an...

ID or keywords:

Entry

Database: PDB / ID: 5w4z

Title

Crystal Structure of Riboflavin Lyase (RcaE) with modified FMN and substrate Riboflavin

Components

Riboflavin Lyase

Keywords

FLAVOPROTEIN /

Cannibalism /

Riboflavin /

Superoxide radical

Function / homology

Function and homology information

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen /

monooxygenase activity /

nucleotide binding
Similarity search - Function

Biological species

Herbiconiux (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Bhandari, D.M. / Chakrabarty, Y. / Zhao, B. / Wood, J. / Li, P. / Begley, T.P.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	DK44083	United States
Robert A. Welch Foundation	A-0034	United States

Citation

Journal: To be Published
Title: Cannibalism Among the Flavins: a Novel C-N Bond Cleavage in Riboflavin Catabolism Mediated by Flavin-Generated Superoxide Radical
Authors: Chakrabarty, Y. / Bhandari, D.M. / Zhao, B. / Wood, J. / Li, P. / Begley, T.P.

History

Deposition	Jun 13, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 13, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5w4z.cif.gz	367.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5w4z.ent.gz	306.1 KB	Display	PDB format
PDBx/mmJSON format	5w4z.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/w4/5w4z ftp://data.pdbj.org/pub/pdb/validation_reports/w4/5w4z	HTTPS FTP

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Related structure data

Related structure data	5w48C 5w4yC 3b9oS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3b9o-d 2vd8-d 3ayf-d 4ecl-2 5g0y-d 6m2i-d 6v82-d 6f04-1 1epv-d 5ca3-2 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	#78 - Jun 2006 Luciferase similarity (3)

Deposited unit

A: Riboflavin Lyase

B: Riboflavin Lyase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	74.970, 108.800, 125.080
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Riboflavin Lyase / RcaE Mass: 50263.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Herbiconiux (bacteria) / Strain: YR403 / Gene: RcaE / Details (production host): pTHT-RcaE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3B6UEK8*PLUS
#2: Chemical	ChemComp-9WY / 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-3-O-phosphono-D-ribitol Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 / Riboflavin Mass: 376.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₀N₄O₆
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.54 Å³/Da / Density % sol: 51.52 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M Bis-Tris-HCl, 1.9 M ammonium sulfate / PH range: 5.8-6.2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2017
Radiation	Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.75→64.3 Å / Num. obs: 102980 / % possible obs: 99.6 % / Redundancy: 8.8 % / B_iso Wilson estimate: 29.8 Å² / R_merge(I) obs: 0.114 / Net I/σ(I): 9
Reflection shell	Resolution: 1.75→1.75 Å / Redundancy: 8.8 % / R_merge(I) obs: 3.591 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1-2155-000	refinement
iMOSFLM	7.2.1	data reduction
PHENIX	1.10.1-2155-000	model building
iMOSFLM	7.2.1	data scaling
PHENIX	1.10.1-2155-000	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B9O

3b9o

Resolution: 1.75→64.3 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.61

	R_factor	Num. reflection	% reflection
R_free	0.207	5136	4.99 %
R_work	0.176	-	-
obs	0.178	102980	99.4 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.75→64.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6887	0	116	379	7382

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7244
X-RAY DIFFRACTION	f_angle_d	0.853	9900
X-RAY DIFFRACTION	f_dihedral_angle_d	14.485	4220
X-RAY DIFFRACTION	f_chiral_restr	0.051	1067
X-RAY DIFFRACTION	f_plane_restr	0.006	1303

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 (%)
1.75-1.7699	0.3919	184	0.3669	3149	X-RAY DIFFRACTION	98
1.7699-1.7907	0.3842	178	0.3357	3196	X-RAY DIFFRACTION	98
1.7907-1.8126	0.3148	140	0.3119	3209	X-RAY DIFFRACTION	98
1.8126-1.8355	0.3042	157	0.2909	3215	X-RAY DIFFRACTION	99
1.8355-1.8597	0.2976	188	0.2746	3179	X-RAY DIFFRACTION	99
1.8597-1.8851	0.2936	152	0.2644	3223	X-RAY DIFFRACTION	99
1.8851-1.9121	0.2962	176	0.2657	3234	X-RAY DIFFRACTION	99
1.9121-1.9406	0.3095	170	0.2515	3180	X-RAY DIFFRACTION	99
1.9406-1.9709	0.2998	170	0.2463	3261	X-RAY DIFFRACTION	99
1.9709-2.0033	0.2761	156	0.229	3205	X-RAY DIFFRACTION	99
2.0033-2.0378	0.2553	169	0.216	3223	X-RAY DIFFRACTION	99
2.0378-2.0749	0.2799	188	0.217	3224	X-RAY DIFFRACTION	100
2.0749-2.1148	0.2318	171	0.2059	3249	X-RAY DIFFRACTION	99
2.1148-2.1579	0.2277	163	0.2029	3225	X-RAY DIFFRACTION	99
2.1579-2.2049	0.2142	160	0.2001	3259	X-RAY DIFFRACTION	99
2.2049-2.2562	0.2411	191	0.1881	3225	X-RAY DIFFRACTION	100
2.2562-2.3126	0.215	189	0.1966	3244	X-RAY DIFFRACTION	100
2.3126-2.3751	0.2332	174	0.1863	3248	X-RAY DIFFRACTION	100
2.3751-2.445	0.2102	160	0.1869	3269	X-RAY DIFFRACTION	100
2.445-2.5239	0.2149	144	0.1805	3304	X-RAY DIFFRACTION	100
2.5239-2.6141	0.2483	172	0.1929	3276	X-RAY DIFFRACTION	100
2.6141-2.7188	0.2393	158	0.1834	3297	X-RAY DIFFRACTION	100
2.7188-2.8425	0.2076	164	0.1911	3285	X-RAY DIFFRACTION	100
2.8425-2.9924	0.1956	201	0.179	3276	X-RAY DIFFRACTION	100
2.9924-3.1799	0.2058	180	0.1706	3283	X-RAY DIFFRACTION	100
3.1799-3.4254	0.1961	155	0.1662	3332	X-RAY DIFFRACTION	100
3.4254-3.7701	0.1683	169	0.1471	3337	X-RAY DIFFRACTION	100
3.7701-4.3155	0.1631	183	0.1355	3331	X-RAY DIFFRACTION	100
4.3155-5.4366	0.176	197	0.1367	3369	X-RAY DIFFRACTION	100
5.4366-64.3474	0.1796	177	0.16	3537	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	2.112	0.0326	0.142	2.4325	0.2684	2.5692	-0.0098	-0.1027	-0.1687	0.4485	0.1945	-0.5837	0.1382	0.4887	-0.1666	0.3797	0.111	-0.1434	0.353	-0.084	0.3926	-121.9218	141.9395	164.9968
2	2.3511	1.3701	-0.5316	3.8637	-0.0168	2.4934	-0.1238	-0.0083	-0.0556	0.1388	0.2548	-0.1875	-0.0372	0.0318	-0.1294	0.3034	0.0752	-0.0535	0.291	-0.0407	0.267	-133.7143	147.9658	160.5836
3	1.4695	0.4536	0.1127	1.9885	0.5271	1.5644	-0.0957	-0.0064	0.2192	-0.0273	0.0971	-0.0747	-0.3028	0.0797	0.0049	0.3499	0.0302	-0.0355	0.2404	-0.048	0.2313	-137.3781	158.8392	155.2111
4	3.1364	0.9971	0.9496	2.383	0.7875	2.5687	-0.1955	0.0486	0.2773	-0.1495	0.1618	-0.1523	-0.4497	0.171	0.0342	0.4333	0.0105	-0.0266	0.2405	-0.0668	0.3014	-134.9208	164.5116	157.4569
5	2.8516	-1.2987	0.985	3.1223	0.1617	2.0084	-0.0394	0.0145	0.0543	0.3962	0.0803	-0.5309	0.0814	0.2021	-0.0439	0.5437	0.0541	-0.1036	0.3898	-0.1048	0.3717	-124.1968	165.1376	175.8028
6	0.9653	0.6565	0.425	0.9783	-0.5769	1.6732	-0.1455	-0.3702	-0.3698	1.0622	0.246	-0.4605	0.2234	0.44	-0.029	0.7088	0.1726	-0.2833	0.5305	-0.0793	0.4888	-119.3924	146.6578	180.4307
7	1.1037	0.9853	0.2393	0.937	0.1641	2.4817	-0.2482	0.1014	0.1378	0.3811	0.212	-1.1842	-0.2305	1.162	-0.0866	0.5405	-0.1115	-0.2605	1.0036	-0.1247	1.1323	-102.9014	151.7748	163.2581
8	1.5806	-0.2506	0.4682	1.1735	0.5365	1.7271	-0.0583	-0.1729	0.0048	0.5228	0.0871	-1.164	-0.4625	1.641	0.0197	0.6451	-0.0612	-0.2817	0.9232	-0.1826	0.8837	-107.9875	155.3131	170.4228
9	1.5017	-0.3811	1.1988	2.0715	-0.4315	2.0645	-0.0663	-0.464	-0.0546	0.8904	0.1447	-0.3434	0.2359	0.0968	-0.0472	0.693	0.1488	-0.2114	0.5506	-0.0848	0.394	-123.7565	150.0072	182.959
10	1.0027	0.1877	1.3211	1.1323	0.377	2.6712	0.0055	-0.6633	0.0121	0.8549	0.004	-0.2644	0.2884	-0.1059	-0.0232	0.8028	0.0642	-0.0709	0.5386	0.0467	0.351	-133.0217	144.0795	183.3363
11	2.1665	0.3275	0.3637	7.0528	-1.1971	3.752	-0.0913	-0.2724	0.2869	0.1956	0.0696	0.2074	-0.0388	-0.2611	0.0167	0.3879	0.0733	-0.0108	0.3355	-0.0944	0.2498	-142.6204	162.813	168.9885
12	1.2487	0.037	0.2807	2.8763	0.5258	1.4279	-0.0541	-0.0197	0.1202	-0.1247	0.0426	0.0788	-0.1836	-0.1517	0.0157	0.2867	0.0151	-0.002	0.3033	-0.021	0.2336	-151.3354	144.6393	145.9645
13	1.4927	0.7822	-0.4279	3.8243	-1.1417	3.9953	-0.0654	0.0371	-0.071	0.1557	0.1599	-0.2957	-0.1456	0.0358	-0.0581	0.2033	0.0267	-0.0192	0.2679	-0.0587	0.2489	-138.1371	140.839	148.7783
14	0.8263	0.1626	-0.4349	2.3436	0.6881	1.9581	-0.0519	0.1347	-0.0535	-0.3085	0.1979	-0.4431	-0.0329	0.4188	-0.0694	0.1958	-0.0475	0.0483	0.3327	-0.1159	0.3154	-126.5474	143.3868	143.6313
15	2.1483	0.5676	0.9878	2.3899	0.1821	3.2268	-0.1183	0.2136	0.0575	-0.3537	0.2339	-0.3999	-0.2741	0.5126	-0.1175	0.304	-0.0457	0.1359	0.3497	-0.1009	0.3364	-125.8318	143.1804	137.0545
16	5.2922	-0.1237	0.6937	2.1067	0.8063	1.8414	-0.0124	0.3433	0.4535	-0.4195	0.0539	-0.0175	-0.1536	0.0149	-0.0367	0.4029	-0.0833	0.0475	0.2487	0.0103	0.2459	-141.3255	134.8259	124.7858
17	1.3897	0.7729	-0.0594	1.8793	-0.0909	1.6197	-0.1771	-0.2244	0.0141	-0.2221	0.1809	0.1974	0.0059	-0.1154	0.0021	0.2915	-0.0289	-0.0517	0.2051	0.0193	0.214	-157.4925	133.9119	135.0571
18	1.6851	0.0353	0.5624	1.3296	-0.5418	3.7159	0.3207	0.5861	0.123	-0.6299	-0.4051	0.2613	-0.7053	-0.0125	0.0338	1.1269	0.0419	-0.1989	0.5495	0.0845	0.6134	-156.4465	157.6516	129.7569
19	1.5494	1.0136	0.0426	2.4007	-0.4483	1.444	-0.3203	0.6728	0.5248	-0.8644	0.387	0.2423	-0.765	-0.0958	-0.0986	0.9619	-0.0452	-0.1174	0.5707	0.0805	0.4968	-154.3219	148.9165	126.6625
20	3.6978	0.6619	-1.212	1.5923	-0.3414	2.1722	-0.2159	0.1368	-0.0661	-0.4144	0.2553	-0.0105	0.0526	-0.0707	-0.0008	0.3223	-0.0255	-0.05	0.2443	0.0317	0.232	-153.9628	129.233	133.8347
21	1.873	2.3328	1.3275	2.9118	1.7539	1.3436	0.079	-0.0349	-0.3265	-0.136	0.0461	-0.0888	0.2486	-0.0774	-0.1834	0.3266	-0.0353	-0.0274	0.2807	0.0901	0.2711	-151.6122	123.0855	142.7294
22	5.1591	1.425	-2.2553	2.5696	-0.2535	3.7968	-0.0739	0.0448	-0.4285	-0.296	0.0737	-0.5744	0.3422	0.6661	0.0409	0.3284	0.0761	0.0776	0.3491	-0.1082	0.4064	-126.6357	129.5023	137.4318

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 4 THROUGH 85 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 86 THROUGH 112 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 113 THROUGH 195 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 196 THROUGH 240 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 241 THROUGH 268 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 269 THROUGH 302 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 303 THROUGH 328 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 329 THROUGH 369 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 370 THROUGH 397 )
10	X-RAY DIFFRACTION	10	CHAIN 'A' AND (RESID 398 THROUGH 425 )
11	X-RAY DIFFRACTION	11	CHAIN 'A' AND (RESID 426 THROUGH 449 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 4 THROUGH 85 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 86 THROUGH 112 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 113 THROUGH 195 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 196 THROUGH 240 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 241 THROUGH 268 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 269 THROUGH 302 )
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESID 303 THROUGH 328 )
19	X-RAY DIFFRACTION	19	CHAIN 'B' AND (RESID 329 THROUGH 369 )
20	X-RAY DIFFRACTION	20	CHAIN 'B' AND (RESID 370 THROUGH 397 )
21	X-RAY DIFFRACTION	21	CHAIN 'B' AND (RESID 398 THROUGH 425 )
22	X-RAY DIFFRACTION	22	CHAIN 'B' AND (RESID 426 THROUGH 450 )

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