PDB-7dnm: Crystal structure of the AgCarB2-C2 complex

ID or keywords:

Entry

Database: PDB / ID: 7dnm

Title

Crystal structure of the AgCarB2-C2 complex

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: 2.3 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	7dnm.cif.gz	450.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7dnm.ent.gz	306.9 KB	Display	PDB format
PDBx/mmJSON format	7dnm.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/7dnm ftp://data.pdbj.org/pub/pdb/validation_reports/dn/7dnm	HTTPS FTP

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Related structure data

Related structure data	7dnnC C: citing same article (ref.)
Similar structure data	7dnn-1 6dmf-1 3wpv-3 6dmf-3 6dmf-10 4ts7-d 6e61-1 6ylz-1 4l7t-d 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 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)	71.702, 100.575, 136.318
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

#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-Gold(DE3)pLysS AG' (bacteria) 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-Gold(DE3)pLysS AG' (bacteria) References: UniProt: H0QPL8
#3: 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
#4: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.17 Å³/Da / Density % sol: 43.2 %
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: BL-17A / Wavelength: 1.85 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2020
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.85 Å / Relative weight: 1
Reflection	Resolution: 2.3→47.18 Å / Num. obs: 81699 / % possible obs: 96.6 % / Redundancy: 6.8 % / B_iso Wilson estimate: 37.64 Å² / R_merge(I) obs: 0.042 / Net I/σ(I): 28.15
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 6.6 % / R_merge(I) obs: 0.265 / Mean I/σ(I) obs: 7.68 / Num. unique obs: 10952

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Processing

Software

Name	Version	Classification
CRANK2		phasing
PHENIX	1.18.2_3874	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.3→47.18 Å / SU ML: 0.241 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.7171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2227	4073	4.99 %
R_work	0.1799	77626	-
obs	0.1821	81699	96.55 %

Solvent computation

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

Displacement parameters

B_iso mean: 40.59 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→47.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7372	0	4	178	7554

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0081	7552
X-RAY DIFFRACTION	f_angle_d	0.9959	10272
X-RAY DIFFRACTION	f_chiral_restr	0.0575	1125
X-RAY DIFFRACTION	f_plane_restr	0.0068	1352
X-RAY DIFFRACTION	f_dihedral_angle_d	8.225	1025

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 (%)
2.3-2.33	0.2936	128	0.223	2422	X-RAY DIFFRACTION	88.2
2.33-2.36	0.2946	131	0.2189	2547	X-RAY DIFFRACTION	91.56
2.36-2.39	0.2653	138	0.2169	2573	X-RAY DIFFRACTION	92.05
2.39-2.42	0.2983	137	0.2094	2594	X-RAY DIFFRACTION	94.04
2.42-2.45	0.2933	133	0.201	2589	X-RAY DIFFRACTION	93.77
2.45-2.48	0.2592	135	0.2101	2598	X-RAY DIFFRACTION	93.85
2.48-2.52	0.2341	144	0.2115	2694	X-RAY DIFFRACTION	95.85
2.52-2.56	0.3129	141	0.205	2626	X-RAY DIFFRACTION	94.89
2.56-2.6	0.2719	136	0.2061	2615	X-RAY DIFFRACTION	96.12
2.6-2.65	0.2877	140	0.2136	2701	X-RAY DIFFRACTION	96.11
2.65-2.7	0.256	140	0.22	2679	X-RAY DIFFRACTION	96.91
2.7-2.75	0.2805	139	0.2206	2689	X-RAY DIFFRACTION	96.19
2.75-2.8	0.2514	142	0.2259	2666	X-RAY DIFFRACTION	97.57
2.8-2.87	0.258	140	0.2245	2689	X-RAY DIFFRACTION	95.96
2.87-2.93	0.2863	143	0.2195	2680	X-RAY DIFFRACTION	98.23
2.93-3	0.2681	146	0.218	2728	X-RAY DIFFRACTION	96.9
3.01-3.09	0.2709	140	0.2149	2693	X-RAY DIFFRACTION	97.52
3.09-3.18	0.2514	144	0.2185	2703	X-RAY DIFFRACTION	98.31
3.18-3.28	0.215	143	0.214	2693	X-RAY DIFFRACTION	96.89
3.28-3.4	0.2109	142	0.2	2719	X-RAY DIFFRACTION	98.11
3.4-3.53	0.231	146	0.1908	2766	X-RAY DIFFRACTION	99.08
3.53-3.69	0.233	142	0.1687	2700	X-RAY DIFFRACTION	98.27
3.69-3.89	0.1926	139	0.152	2738	X-RAY DIFFRACTION	98.26
3.89-4.13	0.1934	142	0.1441	2734	X-RAY DIFFRACTION	98.87
4.13-4.45	0.1752	146	0.1311	2745	X-RAY DIFFRACTION	99.04
4.45-4.9	0.1563	142	0.1325	2737	X-RAY DIFFRACTION	99.1
4.9-5.61	0.1815	142	0.154	2779	X-RAY DIFFRACTION	99.46
5.61-7.06	0.2308	149	0.1813	2774	X-RAY DIFFRACTION	99.76
7.06-47.18	0.1881	143	0.1519	2755	X-RAY DIFFRACTION	99.38

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	1.58962319865	0.643899447625	0.623161700826	0.696613335776	0.368450751218	2.19504299373	-0.106448520667	0.17956714318	0.0653138439552	-0.0395639152991	0.063951667606	-0.232546710478	-0.303129075781	0.15210643232	0.0123305476797	0.297332794559	-0.00603881684068	0.0113078451536	0.30521316898	-0.028201943774	0.314657296884	100.251397042	25.3156585062	55.1754189768
2	1.35312598167	0.339454308359	0.100012910084	1.45803954972	0.202162708605	0.928255468011	0.0179977082182	-0.126395530448	0.170682787147	0.157917562389	0.0281657865862	-0.00869650166067	-0.276786363701	-0.0841661617227	0.0223647415753	0.304409224546	0.00161019876903	0.014286334576	0.271669713625	-0.02413603694	0.246943518108	84.1206214915	27.0828669223	59.7987363644
3	0.921126547282	-0.360343662873	0.213093190579	1.2759859374	-0.0966690150635	0.653054397108	0.0840217812033	0.0468472401194	-0.0502016909057	-0.0503529770647	-0.0357475606506	0.0530717595407	0.0668088067568	-0.110211595973	-0.0157535352747	0.32207982071	-0.0357605086327	-0.0227502499776	0.319514209216	-0.0216658734254	0.299556403547	81.8160075232	19.7232852609	45.3909649768
4	2.48962009227	0.0213878022522	0.655569672066	1.50342740162	0.772649392093	1.90028908245	0.117279958056	-0.0997598794692	-0.0622608898921	0.0207609002147	0.14592191899	0.110564332761	0.00824946885876	-0.144116316881	-0.143035936576	0.464948821302	-0.0892311370461	-0.0200699609795	0.48780812219	-0.0454571407756	0.458565068672	84.7553861002	-4.31447255992	45.0304860011
5	1.17033060666	-0.405187050069	0.758311843107	0.8452552626	0.253013824128	1.13707884252	0.061093101504	0.0421994577955	-0.059840345706	-0.0466568565937	0.0498774663312	-0.158936558575	0.128444130345	0.159241136152	-0.0281809945582	0.295651311615	0.00873813747571	0.0221666490544	0.354552298375	-0.0548746852499	0.335944952904	95.6741573039	15.4687601582	43.5217524312
6	1.67923222394	-1.18404496496	0.607770501508	1.37212139435	-1.066754442	1.84899504512	-0.114687196604	-0.199605748654	-0.0772712700852	0.217106537559	0.0952082803063	0.0580659397724	-0.128918468332	0.0261425145369	-0.068558417901	0.325526808652	0.0139781385859	0.0230304159248	0.245722235572	-0.0231647535468	0.27477541883	87.2037263374	8.18464106212	74.9654992588
7	1.64576673237	-0.557414613087	1.39079408143	0.555892203301	-0.300091667913	1.26051114765	0.16400588429	0.0683622658481	-0.604281548142	0.00180676440089	0.146747308633	0.171007181198	0.116005466097	0.0617348142665	-0.172941221506	0.30642259643	0.00176793862953	-0.000621716514078	0.261724531484	0.00690743671691	0.339913641832	89.3101567633	1.79408556628	71.8532282963
8	0.714492393334	-0.121845216464	-0.468112957292	1.9816724096	0.21345797315	1.26607692677	-0.053885947073	0.119798297784	0.177615772327	-0.289426034932	0.0322324111458	0.0706432094772	-0.24305189817	0.0932001679201	0.0276135771069	0.29459514864	-0.0776100493447	-0.0472895170959	0.327088521847	0.085056726547	0.312391499786	55.3927148851	25.0171433289	9.61187951297
9	0.730151601356	0.575785424252	0.750069572955	0.788239440237	-0.379368512833	1.94806355481	-0.115393718684	0.187172699	0.121060673119	0.0860986021261	0.0537724924354	-0.00337676776562	-0.026141500103	0.350504362915	0.0247057063106	0.287665226195	-0.045039393281	-0.00713048465723	0.360346554928	0.0709695455309	0.341567093381	67.0677767432	21.4270690816	22.1985918649
10	0.640983089771	0.79838945906	0.643851583073	2.1290289849	-0.158469255411	1.82617593693	0.12604313281	0.0911380911458	-0.355187093605	-0.203863577164	0.0750828051943	-0.180204414166	0.496889253375	-0.0159605398409	-0.136010707013	0.479536642556	-0.0203897529433	-0.0191026655247	0.321600091779	0.0118312247618	0.381771728014	52.8118123926	-5.71059588888	20.1031584609
11	1.97228866188	0.295907210235	0.237831755047	2.00285651984	0.198334912601	1.83359008889	-0.0477196912777	-0.0221538727226	0.150013124548	0.0978440077573	-0.00659580785913	0.318551764558	0.136141642289	-0.232049240853	-0.00544199427206	0.274480301098	-0.0171782549571	0.0285176773517	0.302863597377	0.0427173062065	0.325063930515	47.8528632376	16.2068463857	26.2831822519
12	0.964309101289	0.578239638338	0.72755256381	1.32186719973	0.832224114008	1.59649428522	0.0991936801585	0.160842547249	-0.182412710042	-0.250611531076	-0.0250491366307	-0.108027748251	-0.0140956043893	0.131519953382	-0.0608223481814	0.384051994101	0.0358871582426	0.00287266703074	0.404518705055	0.0680475986599	0.355228903343	54.3362409937	4.33692198223	-7.50312975666
13	1.82700888698	-0.301090215486	1.29243526222	1.86614675752	-0.738434184417	2.50426952552	-0.259931449268	0.710422518682	0.438128819711	-0.551902162884	-0.00110136950885	-0.391036643663	-0.669367365061	0.549938921235	-0.0287892360305	0.525004186832	0.00889115583476	0.0662522310021	0.493286628375	0.116468229676	0.457734543998	63.8605851253	10.7874462699	-11.5355906465
14	1.6273756989	0.270113094794	-0.0838241535367	0.242811854877	0.444178045001	1.55847489212	0.143653479201	0.048963875814	-0.341750269983	-0.2241520277	-0.113728047459	-0.211051254584	-0.0783209100644	0.0838126414261	-0.0670479118159	0.347942718251	0.0230688453651	-0.0110752470698	0.356561606537	0.0682934121123	0.355342499815	57.8655902715	5.57732338517	-4.90029496998
15	1.48489031262	0.079721441492	1.77692948426	0.0858883710343	-0.071402031143	2.01294069573	0.190504806209	0.173914022601	-0.105131843734	0.12674135414	-0.0380265873581	-0.237846671145	0.136164244122	-1.35681550591E-5	-0.120139484702	0.383493759717	-0.0317365878382	-0.0217404534062	0.489601770409	0.115626875029	0.370406942591	47.5123389262	-0.649772275436	-6.45059160393

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 40 )	A	A	3 - 40	1 - 38
2	2	chain 'A' and (resid 41 through 115 )	A	A	41 - 115	39 - 113
3	3	chain 'A' and (resid 116 through 201 )	A	A	116 - 201	114 - 199
4	4	chain 'A' and (resid 202 through 232 )	A	A	202 - 232	200 - 230
5	5	chain 'A' and (resid 233 through 338 )	A	A	233 - 338	231 - 336
6	6	chain 'B' and (resid 2 through 87 )	B	B	2 - 87	1 - 86
7	7	chain 'B' and (resid 88 through 134 )	B	B	88 - 134	87 - 133
8	8	chain 'P' and (resid 3 through 115 )	P	C	3 - 115	1 - 113
9	9	chain 'P' and (resid 116 through 183 )	P	C	116 - 183	114 - 181
10	10	chain 'P' and (resid 184 through 254 )	P	C	184 - 254	182 - 252
11	11	chain 'P' and (resid 255 through 338 )	P	C	255 - 338	253 - 336
12	12	chain 'Q' and (resid 2 through 58 )	Q	D	2 - 58	1 - 57
13	13	chain 'Q' and (resid 59 through 70 )	Q	D	59 - 70	58 - 69
14	14	chain 'Q' and (resid 71 through 119 )	Q	D	71 - 119	70 - 118
15	15	chain 'Q' and (resid 120 through 134 )	Q	D	120 - 134	119 - 133

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