PDB-5w4y: Crystal Structure of Riboflavin Lyase (RcaE) with cofactor FMN

ID or keywords:

Entry

Database: PDB / ID: 5w4y

Title

Crystal Structure of Riboflavin Lyase (RcaE) with cofactor FMN

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: 1.9 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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PDBx/mmCIF format	5w4y.cif.gz	507.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5w4y_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5w4y_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5w4y_validation.xml.gz	35.8 KB	Display
Data in CIF	5w4y_validation.cif.gz	51.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w4/5w4y ftp://data.pdbj.org/pub/pdb/validation_reports/w4/5w4y	HTTPS FTP

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Related structure data

Related structure data	5w48C 5w4zC 3b9oS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5w48-d 1yw1-1 6e7c-d 3w7u-1 7bqp-1 3w7w-1 7bqk-d 4j5t-d 4czb-2 2ay7-d 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

101 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)	76.250, 113.470, 117.810
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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.53 Å³/Da / Density % sol: 51.48 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris-HCl, 45% polypropylene glycol P400

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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: 1.9→64.01 Å / Num. obs: 81065 / % possible obs: 99.2 % / Redundancy: 18.6 % / B_iso Wilson estimate: 22.8 Å² / R_merge(I) obs: 0.14 / Net I/σ(I): 13.9
Reflection shell	Resolution: 1.9→1.9 Å / Redundancy: 18.6 % / R_merge(I) obs: 1.75 / % possible all: 97.8

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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: 1.9→64.01 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.23

	R_factor	Num. reflection	% reflection
R_free	0.194	4121	5.08 %
R_work	0.156	-	-
obs	0.158	81065	99.9 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→64.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6910	0	62	377	7349

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	7153
X-RAY DIFFRACTION	f_angle_d	1.017	9757
X-RAY DIFFRACTION	f_dihedral_angle_d	17.034	4195
X-RAY DIFFRACTION	f_chiral_restr	0.058	1057
X-RAY DIFFRACTION	f_plane_restr	0.008	1288

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 (%)
1.9-1.9224	0.382	143	0.3196	2610	X-RAY DIFFRACTION	99
1.9224-1.9458	0.2889	135	0.2637	2599	X-RAY DIFFRACTION	100
1.9458-1.9704	0.2627	135	0.2158	2603	X-RAY DIFFRACTION	100
1.9704-1.9964	0.2814	140	0.2034	2654	X-RAY DIFFRACTION	100
1.9964-2.0237	0.2635	121	0.1951	2628	X-RAY DIFFRACTION	100
2.0237-2.0526	0.2306	131	0.1868	2628	X-RAY DIFFRACTION	100
2.0526-2.0833	0.2022	138	0.1973	2627	X-RAY DIFFRACTION	100
2.0833-2.1158	0.184	127	0.1727	2658	X-RAY DIFFRACTION	100
2.1158-2.1505	0.2165	135	0.1734	2624	X-RAY DIFFRACTION	100
2.1505-2.1876	0.2087	133	0.171	2640	X-RAY DIFFRACTION	100
2.1876-2.2274	0.2466	157	0.1685	2614	X-RAY DIFFRACTION	100
2.2274-2.2702	0.2099	164	0.1924	2603	X-RAY DIFFRACTION	100
2.2702-2.3166	0.1922	152	0.1596	2631	X-RAY DIFFRACTION	100
2.3166-2.3669	0.197	142	0.1537	2615	X-RAY DIFFRACTION	100
2.3669-2.422	0.205	151	0.1512	2622	X-RAY DIFFRACTION	100
2.422-2.4826	0.2091	136	0.1502	2645	X-RAY DIFFRACTION	100
2.4826-2.5497	0.1844	147	0.1531	2646	X-RAY DIFFRACTION	100
2.5497-2.6247	0.2135	141	0.1526	2662	X-RAY DIFFRACTION	100
2.6247-2.7094	0.205	142	0.1647	2627	X-RAY DIFFRACTION	100
2.7094-2.8063	0.2376	148	0.1665	2672	X-RAY DIFFRACTION	100
2.8063-2.9186	0.1793	120	0.1632	2678	X-RAY DIFFRACTION	100
2.9186-3.0515	0.172	135	0.1508	2664	X-RAY DIFFRACTION	100
3.0515-3.2123	0.1848	155	0.1565	2641	X-RAY DIFFRACTION	100
3.2123-3.4136	0.1739	148	0.1573	2665	X-RAY DIFFRACTION	100
3.4136-3.6771	0.1733	159	0.1475	2670	X-RAY DIFFRACTION	100
3.6771-4.0471	0.179	118	0.129	2717	X-RAY DIFFRACTION	100
4.0471-4.6326	0.1521	160	0.1205	2686	X-RAY DIFFRACTION	100
4.6326-5.836	0.1692	149	0.1346	2764	X-RAY DIFFRACTION	100
5.836-64.0487	0.2173	159	0.1651	2851	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	1.6672	0.7476	-0.172	1.5475	0.0125	0.8492	0.0184	-0.131	-0.0725	0.0702	-0.0647	-0.1645	0.0204	0.1179	0.0377	0.1848	0.0022	-0.0368	0.2	-0.006	0.184	47.2995	6.8294	-7.0164
2	1.1413	0.0366	-0.1891	2.7005	-0.0036	1.6133	0.0702	0.0444	0.1124	0.0276	-0.0592	0.6076	-0.0495	-0.3656	-0.069	0.1955	0.0137	-0.0125	0.2739	-0.0291	0.2991	24.9966	11.639	-8.6035
3	1.9787	-0.351	0.411	1.7309	-0.4193	1.0374	0.0574	-0.0457	0.2902	0.3067	-0.0427	-0.0492	-0.2079	0.0969	0.044	0.2347	-0.0395	0.0145	0.2218	-0.0426	0.2283	43.3378	25.7268	0.2662
4	1.2311	0.5306	-0.0582	1.641	-0.0577	2.0856	0.0151	0.0086	-0.067	-0.0237	-0.0424	-0.2821	-0.1719	0.1991	0.0059	0.1738	0.0055	-0.0294	0.2417	0.0029	0.2419	64.3791	24.2987	-13.9369
5	2.0725	0.6639	0.6974	1.6825	0.192	0.9732	0.1607	-0.4838	-0.0408	0.5094	-0.1642	-0.2645	-0.0635	0.1835	-0.0129	0.3703	-0.0774	-0.1035	0.4041	0.0185	0.2359	54.4374	15.4126	10.0847
6	5.0316	-2.3312	3.1994	6.1952	-1.173	6.1358	0.0756	-0.5972	0.025	0.4988	0.0376	0.4279	-0.3415	-0.36	-0.0576	0.2929	-0.0402	0.1094	0.3195	-0.07	0.2274	27.5096	16.8693	6.1565
7	1.7313	0.5303	-0.4617	2.2691	0.0971	1.4778	0.009	-0.1682	-0.1617	0.199	-0.0464	0.3557	0.2343	-0.2069	0.0203	0.2447	-0.0437	-0.0036	0.2296	-0.0017	0.2247	28.7194	-9.3479	-8.4217
8	1.1849	1.2295	0.2963	2.1259	0.5594	0.8113	-0.1515	0.2398	-0.0771	-0.3916	0.1084	0.041	-0.0364	-0.0309	0.0477	0.3358	-0.008	-0.0204	0.2736	-0.0261	0.1968	35.717	-6.5786	-26.46
9	2.3768	0.0942	-1.1091	2.1108	0.8265	2.2092	0.0239	0.1275	-0.109	0.0174	-0.1273	0.6337	0.297	-0.5564	0.0728	0.4507	-0.1538	0.0159	0.4605	-0.0282	0.5587	13.0659	-22.5652	-13.0406
10	1.9314	1.2403	-0.3814	3.3485	-1.194	1.9837	-0.0188	0.0354	-0.4989	0.0895	0.0631	-0.3508	0.3289	0.0636	0.0878	0.4076	0.0414	-0.0149	0.2442	-0.0668	0.4209	39.2373	-23.172	-15.708

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 4 THROUGH 136 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 137 THROUGH 222 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 223 THROUGH 288 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 289 THROUGH 369 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 370 THROUGH 425 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 426 THROUGH 453 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 3 THROUGH 136 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 137 THROUGH 268 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 269 THROUGH 397 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 398 THROUGH 449 )

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