PDB-6v43: Crystal structure of the flavin oxygenase with cofactor and subst...

ID or keywords:

Entry

Database: PDB / ID: 6v43

Title

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

Components

FAD/FMN-containing dehydrogenase

Keywords

OXIDOREDUCTASE / flavin / folate / cofactor / catabolism

Function / homology

Function and homology information

catalytic activity / FAD binding
Similarity search - Function

Biological species

Hoeflea phototrophica (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.77 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 9, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 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
Revision 1.2	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6v43.cif.gz	481.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6v43.ent.gz	326.3 KB	Display	PDB format
PDBx/mmJSON format	6v43.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6v43_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	6v43_full_validation.pdf.gz	1.6 MB	Display
Data in XML	6v43_validation.xml.gz	46.1 KB	Display
Data in CIF	6v43_validation.cif.gz	71.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v4/6v43 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/6v43	HTTPS FTP

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Related structure data

Related structure data	6v42SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6v42-d 3ogs-d 6zjq-d 5jz7-1 6f7v-d 6vep-3 3gj1-d 1xc6-d 1tg7-d 5jqp-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	#117 - Sep 2009 Xanthine Oxidoreductase similarity (4)

Deposited unit

A: FAD/FMN-containing dehydrogenase

B: FAD/FMN-containing dehydrogenase

hetero molecules

107 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)	61.560, 125.380, 127.310
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

#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-LUZ / pteridine-2,4(1H,3H)-dione / Lumazine / 2,4-dihydroxypteridine / 2,4-pteridinediol Mass: 164.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₄N₄O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1131 / 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: 48.12 %
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: 120 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å

Detector

Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 7, 2018

Radiation

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

Radiation wavelength

Wavelength: 1.542 Å / Relative weight: 1

Reflection

Resolution: 1.77→61.56 Å / Num. obs: 90846 / % possible obs: 94.8 % / Redundancy: 6.4 % / B_iso Wilson estimate: 18.66 Å² / CC_1/2: 0.971 / R_merge(I) obs: 0.19 / R_pim(I) all: 0.079 / R_rim(I) all: 0.206 / Net I/σ(I): 6.1 / Num. measured all: 581841 / Scaling rejects: 1735

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.77-1.8	5	0.993	18295	3646	0.605	0.473	1.106	1.4	78.2
9.72-61.56	4	0.216	2786	699	0.923	0.112	0.246	5.6	99.8

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
MOSFLM		data reduction
Aimless	0.5.21	data scaling
PDB_EXTRACT	3.25	data extraction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6V42

6v42

Resolution: 1.77→34.94 Å / SU ML: 0.1867 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7814

	R_factor	Num. reflection	% reflection
R_free	0.2023	4570	5.05 %
R_work	0.1608	-	-
obs	0.1628	90413	94.13 %

Solvent computation

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

Displacement parameters

B_iso mean: 25.17 Å²

Refinement step

Cycle: LAST / Resolution: 1.77→34.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7276	0	130	1131	8537

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0079	7596
X-RAY DIFFRACTION	f_angle_d	0.9505	10328
X-RAY DIFFRACTION	f_chiral_restr	0.0582	1118
X-RAY DIFFRACTION	f_plane_restr	0.0058	1326
X-RAY DIFFRACTION	f_dihedral_angle_d	16.0812	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 (%)
1.77-1.79	0.2966	100	0.2802	2313	X-RAY DIFFRACTION	75.74
1.79-1.82	0.3294	147	0.258	2433	X-RAY DIFFRACTION	80.9
1.82-1.84	0.2563	135	0.2161	2597	X-RAY DIFFRACTION	87.26
1.84-1.86	0.2596	173	0.2073	2620	X-RAY DIFFRACTION	87.5
1.86-1.89	0.2032	162	0.1972	2625	X-RAY DIFFRACTION	88.5
1.89-1.91	0.2459	159	0.1886	2665	X-RAY DIFFRACTION	89.17
1.91-1.94	0.2251	146	0.1927	2703	X-RAY DIFFRACTION	90.5
1.94-1.97	0.2305	159	0.1983	2733	X-RAY DIFFRACTION	90.77
1.97-2	0.2477	140	0.1918	2751	X-RAY DIFFRACTION	91.98
2-2.03	0.2187	141	0.1782	2818	X-RAY DIFFRACTION	93.02
2.03-2.07	0.2394	161	0.1755	2769	X-RAY DIFFRACTION	92.69
2.07-2.1	0.227	135	0.1695	2837	X-RAY DIFFRACTION	93.4
2.1-2.14	0.2	137	0.1686	2860	X-RAY DIFFRACTION	94.48
2.14-2.19	0.2201	162	0.1728	2829	X-RAY DIFFRACTION	94.32
2.19-2.24	0.2296	141	0.1619	2907	X-RAY DIFFRACTION	95.91
2.24-2.29	0.2022	159	0.164	2935	X-RAY DIFFRACTION	96.42
2.29-2.34	0.2262	145	0.1656	2918	X-RAY DIFFRACTION	97.15
2.34-2.41	0.2131	145	0.1705	2973	X-RAY DIFFRACTION	97.41
2.41-2.48	0.2097	146	0.159	2986	X-RAY DIFFRACTION	98.43
2.48-2.56	0.2267	174	0.1612	2995	X-RAY DIFFRACTION	98.66
2.56-2.65	0.2038	157	0.1587	3000	X-RAY DIFFRACTION	99.18
2.65-2.76	0.2104	175	0.1563	2997	X-RAY DIFFRACTION	99.09
2.76-2.88	0.2005	174	0.1571	3012	X-RAY DIFFRACTION	99.56
2.88-3.03	0.202	158	0.1523	3062	X-RAY DIFFRACTION	99.44
3.03-3.22	0.1662	173	0.1463	3032	X-RAY DIFFRACTION	99.47
3.22-3.47	0.1792	136	0.1357	3080	X-RAY DIFFRACTION	99.69
3.47-3.82	0.147	161	0.1318	3078	X-RAY DIFFRACTION	99.6
3.82-4.37	0.1658	166	0.1244	3105	X-RAY DIFFRACTION	99.7
4.37-5.51	0.1663	141	0.1332	3145	X-RAY DIFFRACTION	99.88
5.51-34.94	0.2414	162	0.2136	3065	X-RAY DIFFRACTION	93.19

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	0.914173948307	-0.570166421109	-0.858947040135	2.18674692465	2.43242036618	3.4276956951	-0.0352712302811	0.154948173346	-0.221881474261	0.138317156502	-0.0297540216361	0.0918777257913	0.505301758533	-0.154790105049	0.0502558148828	0.302106100688	-0.0510379516618	-0.0606881622471	0.165286546925	-0.0222636104902	0.226000680385	1.69202486639	-33.1451653106	6.78598454547
2	0.6720426049	0.251300546522	0.273112518041	0.910331342507	0.343704123207	1.06067627727	-0.0391488301509	0.147694936998	-0.0516662351807	-0.198399748435	0.0988606268194	-0.0203500416381	0.137004867051	0.0914120389056	-0.067156244134	0.19448096491	-0.00514540425703	-0.0203414665236	0.172542290166	-0.070901730515	0.158890966066	13.7284300284	-18.1564231009	4.8997151576
3	1.76585641841	0.529235413768	0.12549706215	0.870867948745	0.00556033242433	0.607740843826	0.0243422472275	-0.12827688244	-0.0720796098326	0.119657404044	-0.00405939605862	-0.0381350349778	0.0622468513024	-0.00954267844901	-0.0126302443707	0.0981941499818	0.0141699964476	-0.00522089886127	0.119820196441	-0.0303578968004	0.0999930395642	11.357226902	-7.90869656897	31.9990431049
4	1.92853094141	0.779053255356	-0.27715770883	2.10375072708	-0.408918660876	1.0276415219	-0.0802130637163	0.0086023904926	0.0215616090303	-0.022248158318	0.0292827772636	0.186732538925	0.0507925974089	-0.15586587973	0.0446359435452	0.0726081172639	0.0139841324795	-0.0105262048414	0.167409851453	-0.0322127131568	0.128429093502	-4.66425714419	-4.7694160125	24.4732982685
5	0.812128982841	-0.971107121335	-1.20708194222	1.3657311162	0.870973827013	3.37334524948	0.0183282947908	0.223236781083	-0.00669943221786	-0.311569836518	-0.0821568875418	0.246688510688	0.10376486609	-0.284496450193	0.0407751905721	0.190981820861	-0.0137491911998	-0.0448336635565	0.269751033467	-0.0274453931925	0.219800537994	-4.59002208498	-10.1682380952	10.1532049209
6	2.61405789716	1.06818287088	0.749269846341	3.83646819353	1.29890689542	2.75186310916	-0.0681790356533	0.290492404965	0.283256389303	-0.620547598134	-0.237960132019	0.698646473443	-0.420496329173	-0.570670702884	0.277825600747	0.356449279401	0.0164003626498	-0.111647388694	0.383408009595	0.00237079849917	0.302851268513	-3.11798363763	-11.0560684532	-2.10086622966
7	3.53748770916	-0.548480208712	1.94701380923	2.1540030227	-0.68345901056	1.77991669049	-0.241371649062	0.0366150553204	0.204713715615	0.0555009460236	0.0699806147945	-0.228175457739	-0.299475517099	0.170390338764	0.149984680907	0.169059750184	-0.0579723273782	-0.00503935899875	0.173522903114	-0.0299492854077	0.171461477922	49.4758669273	29.717529444	25.966121992
8	0.636918908479	0.351394067736	0.22177405151	1.14778364645	0.167587101403	0.638977921833	-0.00421977753494	-0.0202154195031	-0.00585906507542	0.106713074307	0.00795712539246	-0.10438694342	-0.0762154555502	0.0599691819308	-0.0111260485247	0.106586325531	-0.00242044123119	-0.025046046847	0.147127079209	-0.0407442270239	0.144951351827	39.0511127347	13.0555764763	27.7945677168
9	0.573633115265	0.203867757298	0.273866410024	1.71710458964	0.367846126618	1.05657457809	-0.159686665191	0.216489481725	0.0973036049655	-0.405755554176	0.0780840352589	0.0520772275594	-0.231411188376	0.10238819139	0.0661915033322	0.253169292561	-0.0431364628003	-0.0625385940722	0.202332307498	-0.00332566094647	0.12921851703	24.9318453449	14.9423583039	2.44346604144
10	0.979537603035	0.08709299193	0.0501134033771	1.09586100277	-0.120521235464	1.03378135038	-0.155966907331	-0.00664356266501	0.336419489761	-0.190098026811	-0.0197839247537	0.29598811596	-0.32775801252	-0.0939099213658	0.127139680329	0.247909804984	0.0270726456432	-0.108760225246	0.147294929157	-0.0218935768816	0.246562552564	20.189602423	28.325402254	16.2173536686
11	4.05952692004	1.19442114994	0.437076842838	4.34735368181	0.828421866905	3.61466534579	0.0223455071195	-0.284392333409	0.301451235938	0.408326624337	-0.167082018184	0.437678758108	-0.416082458162	-0.461738808035	0.106202591512	0.29100635307	0.0345974156871	0.0131885167064	0.231934915624	-0.0755841453231	0.226741182988	28.4462736498	25.8700164637	37.8743306888

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 345 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 346 through 400 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 401 through 421 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 422 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 345 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 346 through 421 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 422 through 466 )

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