PDB-7dnn: Crystal structure of the AgCarB2-C2 complex with homoorientin

ID or keywords:

Entry

Database: PDB / ID: 7dnn

Title

Crystal structure of the AgCarB2-C2 complex with homoorientin

Components

AP_endonuc_2 domain-containing protein
AgCarC2

Keywords

METAL BINDING PROTEIN / C-glycosidase

Function / homology

Function and homology information

Lyases; Carbon-carbon lyases; Other carbon-carbon lyases / lyase activity / metal ion binding
Similarity search - Function

Biological species

Arthrobacter globiformis NBRC 12137 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.25 Å

Authors

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

Funding support

Japan, 1items

Citation

Journal: Nat Commun / Year: 2021
Title: Structural basis for the metabolism of xenobiotic C-glycosides by intestinal bacteria
Authors: Mori, T. / Kumano, T. / He, K. / Awakawa, T. / Watanabe, S. / Hori, S. / Terashita, Y. / Hashimoto, Y. / Senda, M. / Senda, T. / Kobayashi, M. / Abe, I.

History

Deposition	Dec 10, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 20, 2021	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7dnn.cif.gz	458.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7dnn.ent.gz	315.2 KB	Display	PDB format
PDBx/mmJSON format	7dnn.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/dn/7dnn ftp://data.pdbj.org/pub/pdb/validation_reports/dn/7dnn	HTTPS FTP

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Related structure data

Related structure data	7dnmC C: citing same article (ref.)
Similar structure data	7dnm-1 6dmf-10 3wpv-3 6dk2-1 6dmf-1 6dmf-6 6fm9-d 4fym-4 6za4-2 4dwe-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	#74 - Feb 2006 alpha-Amylase similarity (3)

Deposited unit

A: AP_endonuc_2 domain-containing protein

B: AgCarC2

P: AP_endonuc_2 domain-containing protein

Q: AgCarC2

hetero molecules

114 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: AP_endonuc_2 domain-containing protein

B: AgCarC2

hetero molecules

defined by author&software
Evidence: light scattering
57.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

P: AP_endonuc_2 domain-containing protein

Q: AgCarC2

hetero molecules

defined by author&software
57 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.905, 102.511, 136.090
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

Components on special symmetry positions

ID	Model	Components
1	1	A-572- HOH

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Protein , 2 types, 4 molecules APBQ

#1: Protein	AP_endonuc_2 domain-containing protein Mass: 40192.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter globiformis NBRC 12137 (bacteria) Gene: ARGLB_075_00530 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H0QPL9
#2: Protein	AgCarC2 Mass: 16599.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter globiformis NBRC 12137 (bacteria) Gene: ARGLB_075_00520 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H0QPL8

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Non-polymers , 4 types, 178 molecules

#3: Chemical	ChemComp-H9R / 2-[3,4-bis(oxidanyl)phenyl]-6-[(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5,7-bis(oxidanyl)chromen-4-one Mass: 448.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₀O₁₁ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.27 Å³/Da / Density % sol: 45.84 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 25%(w/v) PEG4000, 0.1 M MES pH 6.5, 0.2 M Potassium Iodide

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Data collection

Diffraction	Mean temperature: 95 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 6, 2019
Radiation	Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.25→47.97 Å / Num. obs: 94668 / % possible obs: 99.8 % / Redundancy: 4.2 % / B_iso Wilson estimate: 45.43 Å² / R_merge(I) obs: 0.054 / Net I/σ(I): 17.49
Reflection shell	Resolution: 2.25→2.37 Å / R_merge(I) obs: 0.852 / Num. unique obs: 13699

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Processing

Software

Name	Version	Classification
PHENIX	1.18_3845	refinement
XDS		data reduction
XSCALE		data scaling
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.25→36.17 Å / SU ML: 0.3076 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 27.7391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2471	4737	5 %
R_work	0.1963	89909	-
obs	0.1989	94646	99.83 %

Solvent computation

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

Displacement parameters

B_iso mean: 55.61 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→36.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7319	0	36	173	7528

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7535
X-RAY DIFFRACTION	f_angle_d	0.9354	10264
X-RAY DIFFRACTION	f_chiral_restr	0.0523	1125
X-RAY DIFFRACTION	f_plane_restr	0.0065	1349
X-RAY DIFFRACTION	f_dihedral_angle_d	8.424	1061

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 (%)
2.25-2.28	0.3503	160	0.3021	3018	X-RAY DIFFRACTION	99.87
2.28-2.3	0.3193	158	0.3068	2984	X-RAY DIFFRACTION	99.81
2.3-2.33	0.354	157	0.2968	2984	X-RAY DIFFRACTION	99.94
2.33-2.36	0.3511	159	0.2957	2978	X-RAY DIFFRACTION	99.81
2.36-2.39	0.3299	160	0.2773	3041	X-RAY DIFFRACTION	99.97
2.39-2.42	0.2934	158	0.2782	2975	X-RAY DIFFRACTION	99.94
2.42-2.46	0.3014	159	0.2657	3002	X-RAY DIFFRACTION	99.87
2.46-2.49	0.343	158	0.2712	3006	X-RAY DIFFRACTION	99.81
2.5-2.53	0.31	161	0.2403	2985	X-RAY DIFFRACTION	100
2.53-2.58	0.3043	160	0.2417	3006	X-RAY DIFFRACTION	100
2.58-2.62	0.3213	157	0.246	3004	X-RAY DIFFRACTION	99.91
2.62-2.67	0.314	161	0.2364	2965	X-RAY DIFFRACTION	99.87
2.67-2.72	0.2936	157	0.2545	3037	X-RAY DIFFRACTION	100
2.72-2.77	0.2429	157	0.2511	2997	X-RAY DIFFRACTION	100
2.77-2.83	0.3128	159	0.2406	2989	X-RAY DIFFRACTION	99.9
2.83-2.9	0.3196	156	0.2425	2991	X-RAY DIFFRACTION	99.97
2.9-2.97	0.3295	153	0.2252	3005	X-RAY DIFFRACTION	99.91
2.97-3.05	0.3014	158	0.2327	3009	X-RAY DIFFRACTION	99.97
3.05-3.14	0.2924	157	0.223	2996	X-RAY DIFFRACTION	100
3.14-3.24	0.3028	158	0.2172	3011	X-RAY DIFFRACTION	99.97
3.24-3.36	0.2255	155	0.2193	3003	X-RAY DIFFRACTION	99.94
3.36-3.49	0.2616	154	0.1901	2979	X-RAY DIFFRACTION	99.56
3.49-3.65	0.2484	157	0.1846	2991	X-RAY DIFFRACTION	99.62
3.65-3.85	0.2025	155	0.1749	2987	X-RAY DIFFRACTION	99.78
3.85-4.09	0.2133	159	0.1568	3022	X-RAY DIFFRACTION	99.87
4.09-4.4	0.2126	159	0.1472	2986	X-RAY DIFFRACTION	99.75
4.4-4.84	0.1904	164	0.1444	3003	X-RAY DIFFRACTION	99.81
4.84-5.54	0.1826	156	0.161	2973	X-RAY DIFFRACTION	99.59
5.54-6.97	0.2359	157	0.1915	2992	X-RAY DIFFRACTION	99.4
6.98-36.17	0.192	158	0.1563	2990	X-RAY DIFFRACTION	99.12

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	1.72807362874	0.106073496675	0.196470160098	1.86776453995	-0.522421007879	1.98681582638	-0.117582541779	-0.0324625816441	0.361932644988	0.353315692473	0.0488290173214	-0.203489255163	-0.614960116202	0.165772374652	0.0465141300294	0.456371507878	-0.0158649551874	-0.0475579385253	0.268367229913	-0.0882398324265	0.416245539347	91.8601334004	26.5699808692	58.1323526797
2	1.85006839146	-0.431207179858	-0.0514706140829	1.40450124567	-0.431947500262	5.82928084773	0.028969963438	-0.0335573303411	0.13409090236	-0.0865015187081	0.0338445484401	0.184461734891	-0.207641791707	-0.331175425679	-0.0592897906201	0.296368699852	0.0123565211044	-0.0369852100681	0.26630902571	-0.0166060838744	0.396389978998	80.389476683	24.8600748941	44.9324430043
3	3.11844255336	-1.43867373516	1.31498012293	2.72690952207	-2.54970527815	7.58772697221	0.412211601807	-0.0428855241235	-0.310189888563	0.027003117741	0.205895678341	-0.237043670789	0.630666088962	1.07646789669	-0.689945971917	0.612908086109	0.0920356898315	-0.130136673826	0.48481005349	-0.158020762401	0.561484493194	98.1313105474	-0.0583735978518	49.2566474573
4	1.23219433576	0.029115071895	1.31473280731	2.26352832401	-0.916426261197	2.82089170258	0.195293582052	0.111877532654	-0.482078473815	0.0455765655366	0.0994798946225	0.101175877688	0.800243707365	0.00342392032072	-0.256603104426	0.534161823785	0.0372144519273	-0.0683500315291	0.393037220299	-0.1186059911	0.498062455964	90.318614628	5.08138559184	44.623108584
5	3.39122015002	-0.0713882678626	1.87896419258	2.02358562192	-1.2775769546	5.78815957752	-0.0275140627834	0.355994378604	0.0549432026759	-0.12163420106	-0.0921465737799	-0.456688133542	0.0538072528331	1.03502770095	0.120440144807	0.328925501412	0.0274950938577	0.0293905396913	0.398709110487	-0.0604105529123	0.461911787592	102.052983192	19.365275891	42.7631433207
6	2.54192506962	-0.571755981746	0.174691286591	2.39339533598	-1.55777685474	1.53425646941	-0.336119537392	-0.127351587662	-0.117913714868	0.59949465033	0.269494731369	-0.369697599701	0.282296917651	0.266346312146	0.0330910617464	0.517297160197	0.138726407801	-0.0477005160116	0.344199855768	-0.122006248512	0.354241187236	93.6492176211	7.26186257027	71.9907680527
7	2.18817286943	-1.43496909947	0.568798943908	4.78918899633	-0.267724223831	2.87170277529	-0.254130431914	-0.59129110236	-0.419907237819	0.569669851056	0.373196720374	-0.073170389671	0.514646736999	0.015656891983	-0.126041002118	0.737552439724	0.237628587117	0.0815705415947	0.534273110518	0.02296278644	0.449811741973	88.4663168004	1.27023498725	81.0009852298
8	4.55986129815	3.13214953033	0.388523910357	8.59799298006	0.10488963771	7.33733134783	-0.594456323397	-0.447915063093	0.286481940443	0.88464552931	1.0522617688	0.718894829496	-0.346372329359	-0.729753283645	-0.334373285548	0.578752567791	0.156673343713	0.0601020997468	0.353744567762	-0.0121887364484	0.42130970617	82.7848901296	11.8799021557	78.2847102981
9	2.32608909506	-0.74432079327	0.697275962781	2.77720032195	-1.32716210094	2.42662483598	-0.234050254492	-0.432430960339	0.0704120861314	0.885726717631	0.0546216234519	0.101297394325	-0.248293647407	-0.182451261557	0.146115819351	0.616705015678	0.0724968008882	0.015549058694	0.317700712128	-0.133659168473	0.368122212176	88.8991927818	13.8028305386	74.1187115464
10	3.13386768051	-1.73514119596	3.30184293213	2.07392092232	-1.99481193015	6.0909077825	0.568294441664	-0.654215443187	-1.00412644576	0.0656837932056	0.392787098375	0.573399852339	1.27161015592	0.222558201011	-0.877223845325	0.708239682484	0.218295655457	0.00273196405084	0.490519844182	0.053348307408	0.573219770777	96.5834301041	-1.44316591015	80.0180574664
11	3.93386751554	-0.636476611634	2.84124681179	1.17017419177	-0.522990845521	4.48349263141	0.0329820539865	-0.144432167768	-0.647577607165	0.18374665557	0.289555784466	0.196063697754	0.57897266297	0.346728869994	-0.320306503927	0.439468313815	0.130704359807	0.0517188058123	0.430634838154	-0.0668531219274	0.45753795298	88.0976410896	4.30621631139	64.7297430269
12	1.5412772826	1.13173311625	0.683023023324	2.08762039106	0.408534365937	4.47003756016	-0.472514995138	0.484447580318	0.557035539546	-0.21995280967	0.203784256954	0.173122583963	-0.881662170203	0.233767328074	0.178783633657	0.487281137104	-0.110715023911	-0.146191533094	0.522991662656	0.278758678038	0.539001432776	60.951613388	24.077418945	15.1226639776
13	0.713959521473	2.04026156969	0.41207074762	7.71608279365	2.22854166224	4.30600078355	-0.157506472312	0.301355280933	-0.349883539871	-0.315357746619	0.733457999029	-0.678606592607	0.416156523123	-0.0405917628839	-0.513761770441	0.400653433779	-0.044021982977	-0.0131126981784	0.501308095065	0.0317642894503	0.536885994287	55.1718404966	-5.38724822373	20.0612463214
14	3.21927373297	0.985933270661	0.847855474502	3.45655375654	0.818097132041	3.88086870441	-0.320985747762	0.106410713977	0.39100799481	0.279851755967	0.139058459718	0.755008759549	-0.0888422285226	-0.546692694426	0.218231367007	0.284941075473	0.0622790456773	0.0228062717329	0.418925066559	0.0959901737541	0.484744509724	49.361328618	15.9833044363	26.9668565233
15	0.115960929988	0.65048725042	0.674865420435	3.32409536362	3.32706601377	3.44944900296	0.486785868478	-0.170742714878	-0.253366514636	-0.0466581767813	-0.169702838843	-0.0611900207337	-1.31478334268	-0.787057764393	-0.348714998594	0.561612361675	-0.196097978726	0.0464608935262	0.926702670223	0.181308249925	0.376583373741	50.2802134072	4.74341178885	1.89708754116
16	0.447026220276	0.155824227367	1.1003778599	3.1563771123	-0.249731148959	3.07872765199	-0.664798448958	0.721290576162	0.383436905577	-1.07468636353	0.101829152372	0.0851079275153	0.434531687143	0.195730022482	0.429116092874	0.671674043419	-0.253311981449	-0.0940492121942	0.894178883748	0.217343416827	0.440005649361	48.3140395032	5.48393373672	-14.4942467974
17	1.18730597261	0.180769393799	0.517221057904	1.56857045593	1.39901940974	2.21957218999	-0.249919940552	0.0227102702797	-0.104164397908	-0.113261338347	0.0314558551309	-0.226895173309	-0.090456963573	0.784252797844	0.184333720747	0.473798311949	-0.168060382025	-0.0119151192484	0.76650277652	0.226697611136	0.444248272432	59.969915436	8.75137748548	-1.13191951114
18	1.66851614058	0.537477987342	1.04204710086	0.570560204397	0.0354911452702	0.881561418057	-0.327411869954	1.04669216043	-0.195952053837	-0.705817260139	0.345349565668	-0.410996051034	-0.0271406163448	0.884200203655	0.0735915724238	0.992910995027	-0.343188055536	0.103848062563	1.04291440816	0.060624294818	0.36487111707	58.8878888415	2.48860385828	-14.3594528514
19	3.16189902263	1.45640414711	-1.46128891876	4.29319464381	0.770066344477	4.02051932169	-0.90564295222	0.189130158764	-0.00726040824782	-1.02564271995	0.841594055047	-0.213340226448	-0.856326317308	1.72902120545	0.0257641313831	0.823824902186	-0.357309419026	-0.0111370513541	1.31399613593	0.174868711194	0.422956241392	64.2456734593	12.6506047276	-11.337618023
20	0.62890924005	0.284486212375	-0.444459944864	2.62121497338	0.916730897584	0.789491847784	-0.27800928515	0.57733061806	0.545380544943	-0.36976932209	-0.172434409734	-0.201084277351	-1.20954324184	0.973206164374	0.158944344365	0.576612043427	-0.277580800611	-0.0870825473984	0.939981006249	0.226914629463	0.394211229561	59.8764216074	16.8993674265	-3.37332073283
21	2.1615308751	0.55970189842	0.247146550042	2.53524483911	1.11458594424	1.60350183818	-0.480152160105	0.712986216238	-0.0791771467693	-0.64747804013	0.0599202802151	-0.0415688341548	0.201752881221	0.230327664561	0.386933128465	0.684975480192	-0.260900334286	0.045597887008	0.942941392513	0.0909897011185	0.438718506221	55.254607143	2.56928934011	-8.60782821346
22	5.0912373386	0.5639324819	1.91622702575	0.765480310175	0.189546863789	4.85807285468	0.612129132623	-0.962978616256	-0.94788596946	0.111145336951	-0.218213285642	-0.432685933927	1.02977378707	-0.260399909907	-0.27641094531	0.549921490961	-0.109640043398	0.052921599903	0.646035614228	0.218790387187	0.580763993426	58.2224752122	1.92715533542	-0.451486948133

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 3 through 114 )	A	A	3 - 114	1 - 112
2	2	chain 'A' and (resid 115 through 183 )	A	A	115 - 183	113 - 181
3	3	chain 'A' and (resid 184 through 201 )	A	A	184 - 201	182 - 199
4	4	chain 'A' and (resid 202 through 285 )	A	A	202 - 285	200 - 283
5	5	chain 'A' and (resid 286 through 338 )	A	A	286 - 338	284 - 336
6	6	chain 'B' and (resid 2 through 44 )	B	C	2 - 44	1 - 43
7	7	chain 'B' and (resid 45 through 58 )	B	C	45 - 58	44 - 57
8	8	chain 'B' and (resid 59 through 70 )	B	C	59 - 70	58 - 69
9	9	chain 'B' and (resid 71 through 87 )	B	C	71 - 87	70 - 86
10	10	chain 'B' and (resid 88 through 107 )	B	C	88 - 107	87 - 106
11	11	chain 'B' and (resid 108 through 132 )	B	C	108 - 132	107 - 131
12	12	chain 'P' and (resid 3 through 183 )	P	D	3 - 183	1 - 181
13	13	chain 'P' and (resid 184 through 254 )	P	D	184 - 254	182 - 252
14	14	chain 'P' and (resid 255 through 338 )	P	D	255 - 338	253 - 336
15	15	chain 'Q' and (resid 2 through 9 )	Q	E	2 - 9	1 - 8
16	16	chain 'Q' and (resid 10 through 24 )	Q	E	10 - 24	9 - 23
17	17	chain 'Q' and (resid 25 through 44 )	Q	E	25 - 44	24 - 43
18	18	chain 'Q' and (resid 45 through 58 )	Q	E	45 - 58	44 - 57
19	19	chain 'Q' and (resid 59 through 70 )	Q	E	59 - 70	58 - 69
20	20	chain 'Q' and (resid 71 through 81 )	Q	E	71 - 81	70 - 80
21	21	chain 'Q' and (resid 82 through 112 )	Q	E	82 - 112	81 - 111
22	22	chain 'Q' and (resid 113 through 132 )	Q	E	113 - 132	112 - 131

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