PDB-7dve: Crystal structure of FAD-dependent C-glycoside oxidase

ID or keywords:

Entry

Database: PDB / ID: 7dve

Title

Crystal structure of FAD-dependent C-glycoside oxidase

Components

6'''-hydroxyparomomycin C oxidase

Keywords

OXIDOREDUCTASE / FAD-dependent C-glycoside oxidase

Function / homology

Function and homology information

C-glycoside oxidase / oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function

Biological species

Microbacterium trichothecenolyticum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Senda, M. / Watanabe, S. / Kumano, T. / Kobayashi, M. / Senda, T.

Funding support

Japan, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: FAD-dependent C -glycoside-metabolizing enzymes in microorganisms: Screening, characterization, and crystal structure analysis.
Authors: Kumano, T. / Hori, S. / Watanabe, S. / Terashita, Y. / Yu, H.Y. / Hashimoto, Y. / Senda, T. / Senda, M. / Kobayashi, M.

History

Deposition	Jan 13, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 8, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 2, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7dve.cif.gz	367.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7dve_validation.pdf.gz	749.2 KB	Display	wwPDB validaton report
Full document	7dve_full_validation.pdf.gz	761.9 KB	Display
Data in XML	7dve_validation.xml.gz	29.8 KB	Display
Data in CIF	7dve_validation.cif.gz	41.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dv/7dve ftp://data.pdbj.org/pub/pdb/validation_reports/dv/7dve	HTTPS FTP

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Related structure data

Related structure data	3pl8S S: Starting model for refinement
Similar structure data	5o8e-d 3cnj-d 3b6d-d 6ij9-4 1jjk-8 3cox-d 4cdm-d 4pvk-d 1jjk-7 5o8d-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#77 - May 2006 Glucose Oxidase similarity (4)

Deposited unit

A: 6'''-hydroxyparomomycin C oxidase

B: 6'''-hydroxyparomomycin C oxidase

hetero molecules

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

1

A: 6'''-hydroxyparomomycin C oxidase

hetero molecules

defined by author&software
Evidence: light scattering
57.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 6'''-hydroxyparomomycin C oxidase

hetero molecules

defined by author&software
56.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	267.081, 267.081, 87.209
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	155
Space group name H-M	H32
Space group name Hall	R32"
Symmetry operation	#1: x,y,z #2: -y,x-y,z #3: -x+y,-x,z #4: x-y,-y,-z #5: -x,-x+y,-z #6: y,x,-z #7: x+1/3,y+2/3,z+2/3 #8: -y+1/3,x-y+2/3,z+2/3 #9: -x+y+1/3,-x+2/3,z+2/3 #10: x-y+1/3,-y+2/3,-z+2/3 #11: -x+1/3,-x+y+2/3,-z+2/3 #12: y+1/3,x+2/3,-z+2/3 #13: x+2/3,y+1/3,z+1/3 #14: -y+2/3,x-y+1/3,z+1/3 #15: -x+y+2/3,-x+1/3,z+1/3 #16: x-y+2/3,-y+1/3,-z+1/3 #17: -x+2/3,-x+y+1/3,-z+1/3 #18: y+2/3,x+1/3,-z+1/3

#1: Protein	6'''-hydroxyparomomycin C oxidase Mass: 56332.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microbacterium trichothecenolyticum (bacteria) Gene: livQ_3, RS82_01892 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0M2HFA3, Oxidoreductases; Acting on the CH-OH group of donors; With oxygen as acceptor
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.66 Å³/Da / Density % sol: 53.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 30%(w/v) PEG4000, 0.1 M Tris-HCl pH8.5, 0.2 M Lithium Sulfate

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Data collection

Diffraction	Mean temperature: 95 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.9 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2019
Radiation	Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.9 Å / Relative weight: 1
Reflection	Resolution: 2→48.19 Å / Num. obs: 90727 / % possible obs: 100 % / Redundancy: 6.5 % / B_iso Wilson estimate: 56.51 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 12.42
Reflection shell	Resolution: 2.4→2.53 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.571 / Mean I/σ(I) obs: 3.26 / Num. unique obs: 13294 / % possible all: 100

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
BALBES		phasing
Coot		model building
PHENIX	1.9-4092	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3PL8

3pl8

Resolution: 2.4→48.19 Å / SU ML: 0.3408 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 28.2831
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2572	4539	5 %
R_work	0.2243	86181	-
obs	0.2259	90720	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 78.81 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→48.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5686	0	58	69	5813

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0077	5850
X-RAY DIFFRACTION	f_angle_d	0.9802	7997
X-RAY DIFFRACTION	f_chiral_restr	0.0555	918
X-RAY DIFFRACTION	f_plane_restr	0.0105	1077
X-RAY DIFFRACTION	f_dihedral_angle_d	10.4018	912

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 (%)
2.4-2.43	0.3037	156	0.2906	2878	X-RAY DIFFRACTION	100
2.43-2.46	0.3184	150	0.2821	2854	X-RAY DIFFRACTION	100
2.46-2.49	0.2961	150	0.2773	2877	X-RAY DIFFRACTION	100
2.49-2.52	0.3307	151	0.2662	2853	X-RAY DIFFRACTION	100
2.52-2.55	0.2935	153	0.2681	2880	X-RAY DIFFRACTION	99.97
2.55-2.59	0.3066	153	0.3023	2874	X-RAY DIFFRACTION	100
2.59-2.62	0.3171	153	0.2871	2876	X-RAY DIFFRACTION	100
2.62-2.66	0.3608	152	0.2936	2868	X-RAY DIFFRACTION	100
2.66-2.7	0.3074	153	0.2706	2890	X-RAY DIFFRACTION	100
2.7-2.75	0.2819	150	0.2635	2867	X-RAY DIFFRACTION	99.9
2.75-2.79	0.2619	151	0.2662	2872	X-RAY DIFFRACTION	100
2.79-2.85	0.2818	150	0.2575	2886	X-RAY DIFFRACTION	100
2.85-2.9	0.3507	149	0.2545	2878	X-RAY DIFFRACTION	100
2.9-2.96	0.2831	150	0.2529	2856	X-RAY DIFFRACTION	100
2.96-3.02	0.3315	150	0.264	2882	X-RAY DIFFRACTION	100
3.02-3.09	0.3147	149	0.27	2842	X-RAY DIFFRACTION	100
3.09-3.17	0.3484	149	0.2887	2877	X-RAY DIFFRACTION	99.97
3.17-3.26	0.3014	154	0.2706	2871	X-RAY DIFFRACTION	99.93
3.26-3.35	0.2443	150	0.2436	2897	X-RAY DIFFRACTION	99.97
3.35-3.46	0.3105	152	0.2385	2859	X-RAY DIFFRACTION	100
3.46-3.58	0.2719	150	0.2282	2882	X-RAY DIFFRACTION	100
3.58-3.73	0.2182	150	0.2184	2851	X-RAY DIFFRACTION	99.97
3.73-3.9	0.2435	151	0.21	2882	X-RAY DIFFRACTION	100
3.9-4.1	0.2624	154	0.1894	2876	X-RAY DIFFRACTION	100
4.1-4.36	0.1857	154	0.1772	2885	X-RAY DIFFRACTION	100
4.36-4.7	0.2002	152	0.17	2858	X-RAY DIFFRACTION	100
4.7-5.17	0.211	151	0.1799	2881	X-RAY DIFFRACTION	100
5.17-5.92	0.256	148	0.2188	2866	X-RAY DIFFRACTION	100
5.92-7.45	0.1998	153	0.2211	2880	X-RAY DIFFRACTION	100
7.45-48.19	0.2694	151	0.216	2883	X-RAY DIFFRACTION	99.87

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	1.21776327743	-0.599215773298	-0.278684506365	1.96030347575	1.08763044068	1.11508373	0.44347975433	-0.00506247312697	-0.817371348883	-0.291451447869	0.106924096404	0.593993673424	1.04746169277	0.0375584271796	-0.469948112549	0.80135081968	0.175414132833	-0.390594861764	0.463191678581	-0.0761620571799	0.881459363062	-25.056664646	43.0559717076	15.07988337
2	3.87406307638	0.228638132205	0.94827106518	3.76907338306	-0.238941035882	3.30995749182	-0.00303089848056	-0.590715263101	0.311928802772	0.370756925698	0.158846460401	0.647762691801	0.117479932452	-0.444956701795	-0.193323164263	0.377113364724	0.0491326263967	0.0107008113213	0.502309728414	-0.0320973733741	0.543202168093	-29.0133945028	62.9089777721	26.7340996651
3	1.10517191119	-0.434614292173	0.0767389938121	2.48185383238	-0.576004185459	1.7945141388	0.26444130496	0.135097869043	-0.2785222022	-0.478842945617	0.0454368188383	0.0717273237102	0.429619938191	0.736268268473	-0.279623602968	0.434974449087	0.135604642681	-0.105182099748	0.597060644592	-0.175519579169	0.507045589585	-15.4452663249	62.5384784849	9.14771997195
4	1.15455140857	-0.0691381905834	1.09907787214	6.07695545668	-1.13226981946	3.25687521079	0.261535338453	0.250309751666	-0.318064004524	-0.811613205975	0.0301580713504	0.21201226243	0.354463715791	0.386526365773	-0.281048000176	0.550613386105	0.191862943017	-0.179455369388	0.556945637025	-0.219217612061	0.466622070019	-23.0278931361	62.351350205	3.16684859767
5	1.93161385456	-1.45636224781	-0.0619840149939	5.21820966868	-0.962033563901	2.44965254302	0.17255486006	-0.0897695475765	-0.69120541402	0.172958629814	0.208278778425	0.257106738128	0.957526317971	0.195232232691	-0.387244238162	0.911448675592	0.171878351424	-0.361672081948	0.547587937591	0.00759155010902	0.839604841901	-21.5802649676	37.7914973367	23.1444109936
6	1.80458913377	-0.409354077948	0.597305338465	3.06813547493	-0.364139725701	2.48316807125	0.160355561225	-0.319396469075	-0.513041444138	0.344685753729	0.206211911982	-0.132930313942	1.06445780693	0.422894588481	-0.370798387232	0.812122354777	0.228180944982	-0.271341950982	0.556161626518	-0.0374330189056	0.680679813466	-14.4648483535	43.3612500633	26.4622287681
7	0.0416760031673	0.0170892730419	-0.266819163831	5.67918595614	-0.943159701494	2.71511366195	-0.0627079681846	0.205111286415	0.53842107151	-0.380512082017	0.17988524004	0.518251804206	-0.0966222970405	0.153500663944	-0.183793247099	0.396173572452	-0.00284261772523	-0.0254142161631	0.474911845637	-0.116236151624	0.408486102229	-24.320472074	75.8158106689	10.1687905367
8	2.08476016815	-0.554228918368	0.867115017122	3.72988312156	-0.373062765687	2.45431573232	0.0172987543623	-0.0586117559037	-0.0281890179253	-0.260607285992	0.109459109945	-0.11011740496	-0.0889466681972	0.370878146554	-0.157323431911	0.419299257061	0.0382612778486	-0.0528724981429	0.558944847204	-0.131016934019	0.429722394943	-16.8973022248	73.3880605443	9.58622419669
9	1.23532900521	-0.278071661691	0.329284953259	2.10116074008	-0.238719932435	1.73585572873	0.205450287441	-0.00591376694609	-0.166630506829	0.0266667792836	0.0220837969081	-0.132987048273	0.352666365118	0.750804292458	-0.195718077622	0.389568933065	0.130914899985	-0.122630278913	0.709072133315	-0.2015445817	0.46724483759	-8.69948017645	63.040087696	19.0656280298
10	2.25563618411	-1.14278320588	-1.12966449808	5.52340447279	-0.386108106125	0.751943467706	-0.0407628460413	0.307703468965	-0.806494335322	-0.618947100104	0.185282604791	0.13512558928	1.19461424442	0.333841404186	-0.105093505274	1.05086927209	0.306707697642	-0.232044813163	0.585876557253	-0.232694497413	0.718419543304	-13.3965492797	41.1397186715	6.97541264181
11	3.40497927362	-0.304869006853	-2.20527095041	1.16010201294	0.202871273026	1.42658592024	-0.0832335643507	-0.241706965464	0.0831186315048	0.00108457060808	-0.0946195451986	-0.205433899577	0.0576378117713	0.300901500319	-0.143584106863	0.459036371406	0.453722748802	0.0509544487761	1.90285895096	-0.325657473208	0.763505527303	32.9172099164	63.6761251927	14.7989954464
12	1.82069741419	-0.208353709148	-1.46421336831	1.49880793294	0.553711670738	1.28450272108	0.188596065552	0.0363638247465	-0.501817530307	-0.123062308832	-0.233791200266	0.383357256444	0.194474574772	0.509518122572	0.0894361260155	0.62603216641	0.520612196228	-0.0921713988179	1.95150765427	-0.296325020444	0.858242343667	30.6831270543	53.7120678635	14.728615952
13	0.980337763541	-0.271982583229	-0.176966180559	1.14265672951	0.498820877096	0.214239338979	0.298722501149	0.609470372869	-0.17659045311	-0.327960793743	-0.139543710844	-0.105356904685	0.254018693327	0.626688171316	-0.0741658955977	0.631978757633	0.714968637402	-0.0039297389932	2.38222480422	-0.368808234834	0.95618857294	27.9733478997	54.3256783335	13.5066383335
14	3.39911795838	-0.0385280891839	-0.843853014002	1.94963808909	-0.93916476025	1.13112211325	0.23331638118	0.308413146128	0.00874246011628	-0.0379880543837	-0.222698500463	-0.360131548463	0.0178959578766	0.813183074311	0.0664965350706	0.502092985605	0.376303462227	-0.149448179806	1.93986062212	-0.30660232555	0.688846914641	22.1369745763	64.3763193214	24.4513289782
15	3.33708951746	-2.2053161192	-1.12447323513	2.31818482171	0.461670346758	0.469441788055	0.294203556171	0.629397649181	-0.874776994086	-0.459183963997	-0.371922254128	0.279295416587	0.250123633438	0.0811609438671	0.0735168822438	0.994548018226	0.842830767877	-0.374213757838	1.5588728456	-0.353723627278	1.30645425918	17.5579250206	35.7351789869	23.3743270669
16	2.07337422306	0.372150929218	-1.06277957578	2.74636039967	-1.27800270544	0.998963455437	0.483423531246	-0.583494765727	-0.341647780634	0.371712619625	-0.518109904251	0.0514107112047	0.192810973343	0.475282191733	0.0117791107421	0.781121224744	0.445487024715	-0.287540211914	1.45292558844	-0.271850051499	0.833297824002	15.0742117533	46.5557084714	32.3512566905
17	0.151368787283	-0.117852594299	-0.176392692053	2.87179916682	1.32228498308	0.703235340764	-0.297578322784	0.00455941141995	-0.195884611453	0.191212558491	-0.0159669303074	-0.397514640743	0.115301470933	0.0370699982529	0.0858374637504	0.713918783527	0.577668558113	-0.120275931639	1.60118738611	-0.345004719967	0.759334541469	13.7766784894	52.3547910487	19.4732016719
18	5.31166424372	-1.15824339539	-0.255700572924	1.01243066693	0.341089534477	0.114163216061	0.181420814281	0.52266792707	-0.202484723332	-0.248609119455	-0.184001815291	-0.126661903785	0.220436690771	0.42548977942	0.0467825707797	0.695181166004	0.705310613725	-0.204428170596	2.04740842567	-0.430003350829	0.718058874034	20.4262422558	55.5723118084	12.2059279241

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 5 through 53 )	A	A	5 - 53	1 - 49
2	2	chain 'A' and (resid 54 through 101 )	A	A	54 - 101	50 - 86
3	3	chain 'A' and (resid 102 through 184 )	A	A	102 - 184	87 - 169
4	4	chain 'A' and (resid 185 through 224 )	A	A	185 - 224	170 - 209
5	5	chain 'A' and (resid 225 through 254 )	A	A	225 - 254	210 - 239
6	6	chain 'A' and (resid 255 through 293 )	A	A	255 - 293	240 - 278
7	7	chain 'A' and (resid 294 through 327 )	A	A	294 - 327	279 - 312
8	8	chain 'A' and (resid 328 through 359 )	A	A	328 - 359	313 - 344
9	9	chain 'A' and (resid 360 through 489 )	A	A	360 - 489	345 - 474
10	10	chain 'A' and (resid 490 through 513 )	A	A	490 - 513	475 - 498
11	11	chain 'B' and (resid 4 through 29 )	B	C	4 - 29	1 - 26
12	12	chain 'B' and (resid 30 through 136 )	B	C	30 - 136	27 - 44
13	13	chain 'B' and (resid 137 through 254 )	B	C	137 - 254	45 - 119
14	14	chain 'B' and (resid 255 through 294 )	B	C	255 - 294	120 - 159
15	15	chain 'B' and (resid 295 through 374 )	B	C	295 - 374	160 - 179
16	16	chain 'B' and (resid 375 through 424 )	B	C	375 - 424	180 - 229
17	17	chain 'B' and (resid 425 through 461 )	B	C	425 - 461	230 - 249
18	18	chain 'B' and (resid 462 through 511 )	B	C	462 - 511	250 - 299

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