PDB-6v42: Crystal structure of the flavin oxygenase with cofactor bound inv...

ID or keywords:

Entry

Database: PDB / ID: 6v42

Title

Crystal structure of the flavin oxygenase with cofactor bound involved in folate catabolism

Components

FAD/FMN-containing dehydrogenase

Keywords

OXIDOREDUCTASE / flavin / folate / cofactor / catabolism

Function / homology

Function and homology information

lactate catabolic process / D-lactate dehydrogenase (cytochrome) activity / D-lactate dehydrogenase (NAD+) activity / FAD binding
Similarity search - Function

Biological species

Hoeflea phototrophica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.45 Å

Authors

Begley, T.P. / Adak, S. / Zhao, B. / Li, P.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: A novel flavoenzyme catalyzed Baeyer-Villiger type rearrangement in bacterial folic acid catabolic pathway
Authors: Begley, T.P. / Adak, S. / Zhao, B. / Li, P.

History

Deposition	Nov 27, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 2, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6v42.cif.gz	478.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6v42.ent.gz	324.3 KB	Display	PDB format
PDBx/mmJSON format	6v42.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6v42_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	6v42_full_validation.pdf.gz	1 MB	Display
Data in XML	6v42_validation.xml.gz	44.6 KB	Display
Data in CIF	6v42_validation.cif.gz	69.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v4/6v42 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/6v42	HTTPS FTP

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Related structure data

Related structure data	6v43C C: citing same article (ref.)
Similar structure data	6v43-d 1d1c-d 6fz5-d 3iwe-d 5o6j-d 6sk2-d 1mmd-d 7dmu-1 3tw9-2 2wyn-1 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	#117 - Sep 2009 Xanthine Oxidoreductase similarity (4)

Deposited unit

A: FAD/FMN-containing dehydrogenase

B: FAD/FMN-containing dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: mass spectrometry

Unit cell

Length a, b, c (Å)	61.669, 125.209, 127.329
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	FAD/FMN-containing dehydrogenase Mass: 52412.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hoeflea phototrophica (strain DSM 17068 / NCIMB 14078 / DFL-43) (bacteria) Strain: DSM 17068 / NCIMB 14078 / DFL-43 / Gene: HPDFL43_08194 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A9D9D1
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1125 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.15 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M TRIS hydrochloride pH 8.5, 2.0M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9776 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9776 Å / Relative weight: 1
Reflection	Resolution: 1.45→56.75 Å / Num. obs: 173949 / % possible obs: 99.6 % / Redundancy: 6.7 % / B_iso Wilson estimate: 16.58 Å² / R_merge(I) obs: 0.063 / R_rim(I) all: 0.068 / Net I/σ(I): 14.1
Reflection shell	Resolution: 1.45→1.47 Å / Num. unique obs: 8569 / CC_1/2: 0.83

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
Aimless		data scaling
PHENIX	1.13_2998	refinement
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.45→50.74 Å / SU ML: 0.1378 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.2612

	R_factor	Num. reflection	% reflection
R_free	0.1755	8853	5.09 %
R_work	0.1522	-	-
obs	0.1534	173850	99.5 %

Solvent computation

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

Displacement parameters

B_iso mean: 23.21 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→50.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7276	0	106	1125	8507

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0083	7570
X-RAY DIFFRACTION	f_angle_d	0.9975	10292
X-RAY DIFFRACTION	f_chiral_restr	0.0829	1118
X-RAY DIFFRACTION	f_plane_restr	0.0059	1324
X-RAY DIFFRACTION	f_dihedral_angle_d	16.0867	2730

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 (%)
1.45-1.47	0.2973	321	0.2375	5467	X-RAY DIFFRACTION	99.52
1.47-1.48	0.2328	280	0.2238	5391	X-RAY DIFFRACTION	99.21
1.48-1.5	0.2326	297	0.2034	5493	X-RAY DIFFRACTION	99.48
1.5-1.52	0.2179	284	0.2018	5374	X-RAY DIFFRACTION	98.92
1.52-1.54	0.2318	302	0.1963	5485	X-RAY DIFFRACTION	99.55
1.54-1.56	0.2183	277	0.1875	5439	X-RAY DIFFRACTION	99.65
1.56-1.58	0.206	260	0.1794	5508	X-RAY DIFFRACTION	99.47
1.58-1.61	0.1811	297	0.1712	5416	X-RAY DIFFRACTION	99.56
1.61-1.63	0.2059	285	0.1712	5465	X-RAY DIFFRACTION	99.65
1.63-1.66	0.1975	303	0.1627	5466	X-RAY DIFFRACTION	99.57
1.66-1.69	0.1845	300	0.164	5445	X-RAY DIFFRACTION	99.79
1.69-1.72	0.2202	325	0.1807	5461	X-RAY DIFFRACTION	99.72
1.72-1.75	0.202	276	0.171	5478	X-RAY DIFFRACTION	99.77
1.75-1.79	0.1956	294	0.1634	5477	X-RAY DIFFRACTION	99.6
1.79-1.83	0.186	288	0.1561	5475	X-RAY DIFFRACTION	99.55
1.83-1.87	0.1865	291	0.1523	5504	X-RAY DIFFRACTION	99.64
1.87-1.92	0.188	306	0.1503	5445	X-RAY DIFFRACTION	99.53
1.92-1.97	0.1835	307	0.1488	5430	X-RAY DIFFRACTION	98.64
1.97-2.03	0.1682	263	0.1488	5482	X-RAY DIFFRACTION	98.97
2.03-2.09	0.1658	278	0.1481	5500	X-RAY DIFFRACTION	99.69
2.09-2.17	0.1647	286	0.1464	5507	X-RAY DIFFRACTION	99.86
2.17-2.25	0.1769	289	0.1442	5542	X-RAY DIFFRACTION	99.73
2.25-2.36	0.1638	333	0.1443	5486	X-RAY DIFFRACTION	99.78
2.36-2.48	0.1703	385	0.1475	5457	X-RAY DIFFRACTION	99.76
2.48-2.63	0.1721	293	0.1489	5532	X-RAY DIFFRACTION	99.85
2.63-2.84	0.1802	279	0.1535	5602	X-RAY DIFFRACTION	99.98
2.84-3.12	0.167	307	0.1489	5582	X-RAY DIFFRACTION	99.93
3.12-3.58	0.1596	286	0.1394	5485	X-RAY DIFFRACTION	97.3
3.58-4.5	0.1411	302	0.1261	5653	X-RAY DIFFRACTION	99.52
4.51-50.74	0.1771	259	0.1579	5950	X-RAY DIFFRACTION	99.9

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	0.761165932268	-0.634541670136	-0.791183147183	1.64449459398	2.26853158862	3.03273095679	-0.106040401699	0.128438422035	-0.222936794332	0.270209537568	0.0131832945586	0.0594738142399	0.632700664605	-0.119223020606	0.0996137829626	0.313674599139	-0.0451538852444	-0.0410896508804	0.15808818126	-0.0241085443063	0.23926701831	1.79591904817	-33.1559725289	6.75994285237
2	0.650584936202	0.197915506372	0.309222197177	0.612428361658	0.314996983556	0.852618534442	-0.00824107472893	0.160741618082	-0.0864899000726	-0.149483370208	0.104733221513	-0.0479207060551	0.107602316063	0.10870053186	-0.0936474285559	0.179869542658	0.00134172433675	-0.021497729881	0.160501036285	-0.0585683279159	0.144877266596	13.8313087603	-18.1972635632	4.89001877945
3	2.02537259278	0.655662265269	-0.398317398582	1.09585930304	-0.114371407674	0.902131579835	0.0244955297374	-0.160146306528	-0.0573826302134	0.119573539607	-0.0158565252941	-0.0371870078707	0.064947515021	0.0135902851039	-0.00662648568593	0.0959462170885	0.0145533447304	-0.0207311835526	0.12224043489	-0.0240117630448	0.0807071634709	14.5481307478	-6.31943799068	34.2317997509
4	1.15912931792	-0.00865576141895	0.199550532225	1.26774139907	0.188775499827	0.586928441263	-0.00182498269368	-0.0142329530108	-0.007211525215	-0.00776757612538	0.0041082011807	0.161797095625	0.0479183239064	-0.115769576508	-0.00706677913186	0.0825029777515	0.0031680844332	-0.00550104772439	0.131244360102	-0.0194736399134	0.108430910313	-2.44763501634	-7.98633421434	23.7632399641
5	4.86560254881	-0.86207085698	-4.81947023567	6.11729303424	3.64030622713	7.227083243	0.0632462164865	0.350947486052	0.209916312038	-0.641253357632	-0.0511184413538	0.0601160408194	-0.794578238945	-0.243042921416	-0.0104159777667	0.26138512169	-0.00117678769274	-0.0719105861942	0.236598531378	0.0123597908669	0.2227443386	-0.865561177521	-10.6292169201	-1.3079425652
6	3.10932837642	0.673565698162	-0.402498457867	4.38707113214	-0.127427600421	2.31889447324	0.0858825425615	0.208884680424	0.75885247195	-0.131093293575	-0.26832810881	0.614387872193	-0.857113303899	-0.464010290389	0.222274604773	0.449055634318	0.0363469608523	-0.0758294339524	0.317405753929	-0.00709086415113	0.352317133715	-4.17946177337	-10.9256962127	-0.565526504584
7	2.86964481927	-0.380149146796	1.60682755955	1.71578613663	-0.531647170866	1.55775114327	-0.219810354787	0.0557675083384	0.191873846257	0.007931078488	0.0737743886639	-0.200825748541	-0.265317076275	0.135027065794	0.155841872129	0.161846455797	-0.053159982666	-0.00351488045192	0.15194050837	-0.0281300887798	0.171038625187	49.5361888059	29.6436045958	25.9914825958
8	0.576231154127	0.242105506464	0.317292012943	1.08428156492	0.161441309767	0.605674039577	-0.0258628885308	-0.0301436227683	-0.0177761480858	0.081253981816	0.0285202947485	-0.127671856548	-0.0745334008528	0.0572757194994	-0.0108350128384	0.095864052716	-0.00783237682638	-0.0149035237706	0.13087412155	-0.0366836464742	0.124698241077	39.1293792373	12.969940945	27.823340522
9	0.837952597996	0.0278087236226	0.396273720516	2.1009027995	-0.139969686979	1.54027599734	-0.148694463756	0.244671120019	0.09934359463	-0.353193628281	0.0658600425786	0.0330745205433	-0.24940113162	0.10804010223	0.0716067705916	0.237549443055	-0.0438703246968	-0.0534180331038	0.191288185366	-0.00955524560889	0.102879669889	22.8530586392	12.2308959991	1.04787586449
10	1.13784118783	0.171281383776	-0.0967530619854	1.82154240902	0.577911675206	1.44341345894	-0.187860955499	0.213514179338	0.0664844758164	-0.412460445054	0.136684881708	-0.0223759569033	-0.240604246379	0.220556295794	0.0535667232179	0.245041312678	-0.0706188885409	-0.0466596012902	0.180210499042	0.0187173272181	0.102609362959	28.4430517185	18.9781587632	4.55931984862
11	1.89527332979	-0.330533505324	0.153624792417	3.08748297321	-2.06301285469	2.92128203767	-0.201370396352	0.154459521017	0.332175900509	-0.103163182569	0.0676808477076	0.39079271951	-0.385796200495	-0.158552123274	0.0672926116302	0.241298420816	0.00236043596089	-0.142136035663	0.153915597629	-0.0212807239073	0.220728061309	16.0746667379	25.0358662778	9.72353508173
12	0.700477445426	0.0111311217212	0.197641714323	0.359457325295	0.0113686619284	0.997229977931	-0.175559720263	-0.0136797853691	0.342764104797	-0.179239127335	-0.0041717849303	0.156619446764	-0.344743396308	-0.00575305937826	0.142572028103	0.246761450037	0.00861771261227	-0.105585642046	0.13571557832	-0.00992802523234	0.257528106023	21.5763109451	30.894924327	16.8720179283
13	3.76101616273	-0.540155347612	0.73008898363	3.52702270267	-0.573138744541	3.353513306	-0.136773228575	-0.38809280126	0.0663500194019	0.452465674401	0.0193156076364	0.103200914439	-0.348965084868	-0.390478327486	0.101362997761	0.179823212374	0.0197463012458	0.00223935591317	0.127892643286	-0.0505110378963	0.124275247489	28.6419819488	23.6600800166	36.7989424451
14	2.8930544018	0.610550395715	0.439381398045	3.2417595707	0.738165524035	2.83087799619	-0.0233150334456	-0.313512507941	0.365007008983	0.137032094212	-0.142299810379	0.528928320877	-0.297433041508	-0.50461916617	0.151241253525	0.227714691482	0.0408156998465	-0.0122775491267	0.212846064051	-0.0671316840225	0.230977240528	27.7273272174	27.0423845224	36.5040723592

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 55 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 56 through 215 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 216 through 314 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 315 through 411 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 412 through 431 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 432 through 466 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 55 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 56 through 215 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 216 through 294 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 295 through 345 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 346 through 370 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 371 through 411 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 412 through 431 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 432 through 466 )

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