PDB-9du6: Crystal structure of ADP-ribose diphosphatase from Klebsiella pne...

ID or keywords:

Entry

Database: PDB / ID: 9du6

Title

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ATP bound)

Components

ADP-ribose pyrophosphatase

Keywords

HYDROLASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / ADP-ribose diphosphatase

Function / homology

Function and homology information

ADP-sugar diphosphatase activity / ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / nucleotide binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ATP bound)
Authors: Mian, M.R. / Liu, L. / Lovell, S. / Buchko, G.W. / Battaile, K.P.

History

Deposition	Oct 2, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 16, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9du6.cif.gz	178.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9du6.ent.gz	140.5 KB	Display	PDB format
PDBx/mmJSON format	9du6.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/du/9du6 ftp://data.pdbj.org/pub/pdb/validation_reports/du/9du6	HTTPS FTP

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Related structure data

Similar structure data	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	#145 - Jan 2012 Messenger RNA Capping similarity (6) #201 - Sep 2016 Isoprene Synthase similarity (4)

Deposited unit

A: ADP-ribose pyrophosphatase

B: ADP-ribose pyrophosphatase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	57.934, 80.392, 92.888
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	ADP-ribose pyrophosphatase / ADP-ribose diphosphatase / ADP-ribose phosphohydrolase / Adenosine diphosphoribose pyrophosphatase Mass: 24742.848 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPHS_45750 / Plasmid: KlpnC.20447.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3GVQ7, ADP-ribose diphosphatase
#2: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.72 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% (v/v) PEG 3350, 0.2M sodium acetate, 0.1 M Tris 8.4, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 CD/34. 5 hour soak in 2mM ATP, Puck: PSL-1504, Cryo: 30% (v/v) PEG 3350, 0.2 M ...Details: 25% (v/v) PEG 3350, 0.2M sodium acetate, 0.1 M Tris 8.4, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 CD/34. 5 hour soak in 2mM ATP, Puck: PSL-1504, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.4.

Crystal

Density Matthews: 2.19 Å³/Da / Density % sol: 43.72 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% (v/v) PEG 3350, 0.2M sodium acetate, 0.1 M Tris 8.4, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 CD/34. 5 hour soak in 2mM ATP, Puck: PSL-1504, Cryo: 30% (v/v) PEG 3350, 0.2 M ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 3, 2024
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.55→49.16 Å / Num. obs: 63707 / % possible obs: 100 % / Redundancy: 13.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.064 / R_pim(I) all: 0.018 / R_rim(I) all: 0.067 / Χ²: 1.01 / Net I/σ(I): 18.2 / Num. measured all: 853652
Reflection shell	Resolution: 1.55→1.58 Å / % possible obs: 100 % / Redundancy: 13.7 % / R_merge(I) obs: 1.296 / Num. measured all: 42533 / Num. unique obs: 3113 / CC_1/2: 0.813 / R_pim(I) all: 0.362 / R_rim(I) all: 1.347 / Χ²: 1.11 / Net I/σ(I) obs: 2.1

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Processing

Software

Name	Version	Classification
PHENIX	(dev_5295: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.55→49.16 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2024	3117	4.9 %
R_work	0.1723	-	-
obs	0.1737	63593	99.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.55→49.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3079	0	31	260	3370

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3227
X-RAY DIFFRACTION	f_angle_d	1.026	4389
X-RAY DIFFRACTION	f_dihedral_angle_d	15.075	1200
X-RAY DIFFRACTION	f_chiral_restr	0.067	485
X-RAY DIFFRACTION	f_plane_restr	0.01	570

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 (%)
1.55-1.57	0.3314	118	0.3143	2705	X-RAY DIFFRACTION	100
1.57-1.6	0.3655	165	0.2937	2702	X-RAY DIFFRACTION	100
1.6-1.63	0.2787	162	0.2567	2677	X-RAY DIFFRACTION	100
1.63-1.66	0.2744	125	0.2193	2750	X-RAY DIFFRACTION	100
1.66-1.69	0.2046	140	0.1964	2688	X-RAY DIFFRACTION	100
1.69-1.72	0.2232	143	0.183	2720	X-RAY DIFFRACTION	100
1.72-1.76	0.1993	140	0.1748	2727	X-RAY DIFFRACTION	100
1.76-1.8	0.2088	147	0.1829	2722	X-RAY DIFFRACTION	100
1.8-1.85	0.2065	144	0.1885	2683	X-RAY DIFFRACTION	100
1.85-1.9	0.2084	140	0.1967	2740	X-RAY DIFFRACTION	100
1.9-1.95	0.2595	159	0.2095	2730	X-RAY DIFFRACTION	100
1.95-2.02	0.2221	151	0.1878	2712	X-RAY DIFFRACTION	100
2.02-2.09	0.1953	137	0.1784	2739	X-RAY DIFFRACTION	100
2.09-2.17	0.2361	139	0.162	2744	X-RAY DIFFRACTION	100
2.17-2.27	0.1903	112	0.166	2766	X-RAY DIFFRACTION	100
2.27-2.39	0.195	129	0.172	2766	X-RAY DIFFRACTION	100
2.39-2.54	0.2087	136	0.1674	2763	X-RAY DIFFRACTION	100
2.54-2.74	0.1978	148	0.1687	2790	X-RAY DIFFRACTION	100
2.74-3.01	0.2069	123	0.177	2784	X-RAY DIFFRACTION	100
3.01-3.45	0.195	146	0.177	2794	X-RAY DIFFRACTION	100
3.45-4.34	0.181	161	0.1473	2807	X-RAY DIFFRACTION	100
4.34-49.16	0.191	152	0.163	2967	X-RAY DIFFRACTION	100

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	8.159	3.8011	-3.915	8.5235	-3.9916	5.2249	-0.2433	-0.0621	-0.3638	-0.2742	0.1611	0.2507	0.2401	-0.135	-0.0242	0.2263	-0.0053	-0.0138	0.3405	-0.0449	0.2381	-23.6431	-1.8838	-19.9446
2	7.858	4.4349	-4.5006	4.6097	-3.3382	5.9274	-0.318	0.1981	0.1499	-0.4916	0.2071	0.2093	0.1423	-0.326	0.0399	0.2492	0.0298	-0.0365	0.2298	-0.0126	0.1772	-20.9126	4.9645	-20.8459
3	5.6895	-2.8978	0.9765	2.6266	-0.5029	1.2056	0.0389	0.2668	0.1803	-0.1411	-0.0607	-0.2538	-0.0075	0.0883	0.0061	0.2161	-0.0246	0.0252	0.1722	-0.0208	0.1798	-3.5091	1.3413	-19.6559
4	3.3981	-4.3817	1.1985	6.9397	-1.8932	1.0089	0.0322	0.0316	0.1868	-0.0981	0.0691	-0.3627	-0.0378	0.1805	-0.0903	0.1858	-0.0264	0.0241	0.2424	-0.0213	0.2988	11.9723	7.7036	-16.139
5	4.449	3.956	4.2167	3.6793	3.7849	4.1164	-0.0347	0.8496	0.1632	-0.3843	0.2266	0.0649	0.0688	0.2002	-0.1754	0.3661	-0.0097	0.0203	0.4203	-0.0527	0.3094	2.937	-4.3945	-25.0035
6	2.8962	2.9656	0.9321	4.2535	1.979	7.7576	0.194	0.9493	-0.3043	-0.1974	-0.0489	-0.187	-0.1256	-0.0323	-0.1146	0.373	-0.0012	0.0742	0.2497	-0.0061	0.3079	9.4512	-6.8865	-25.6674
7	6.7253	-2.972	-0.0558	3.1896	0.3623	1.0557	-0.0706	0.035	-0.3433	0.0138	0.1844	-0.0688	0.0854	0.0443	-0.1227	0.1998	-0.0088	0.0174	0.1733	-0.0392	0.2161	2.5149	-5.7539	-16.5184
8	2.6008	-2.2503	1.6807	6.7165	-1.3694	3.3095	0.3576	0.9525	-0.0915	-0.9373	-0.5541	-0.6242	-0.4235	1.3063	0.2448	0.4533	-0.0482	0.1175	0.5757	-0.0839	0.4862	20.6189	-1.5416	-23.2179
9	3.4991	-0.5485	-0.2762	3.4774	-0.0577	2.7083	0.0118	-0.1443	-0.0095	0.2577	0.0429	-0.2447	0.0209	0.266	-0.0561	0.1669	0.0052	-0.0276	0.208	-0.0291	0.2328	12.4584	-2.4054	-7.0764
10	7.3526	-2.0255	2.3974	4.6123	-1.6883	2.9041	-0.3695	0.1219	0.8207	0.2186	-0.0627	-0.9388	-0.428	0.4926	0.4765	0.3777	-0.0624	0.0453	0.3033	0.0432	0.4723	9.3939	20.5519	-22.4851
11	2.4593	-0.5831	0.5763	2.1964	-0.7871	1.9734	-0.1382	-0.0574	0.4143	-0.282	-0.0148	-0.0436	-0.0182	0.1598	0.1217	0.3313	-0.0135	0.0336	0.2021	0.0494	0.2846	-4.1041	18.3838	-26.1178
12	1.517	-0.503	-0.8316	1.8589	2.1067	2.4372	-0.2011	0.9154	0.4592	-0.4827	-0.543	-1.1649	-0.2858	1.2688	-0.1332	0.4617	0.0437	0.2508	0.697	0.2436	0.7282	17.1797	16.5692	-29.1061
13	1.0009	0.3847	-0.1144	2.7001	-2.2286	3.547	-0.0164	-0.0157	0.1509	-0.1005	0.0772	-0.0949	-0.0052	-0.2067	-0.0486	0.2002	0.0227	0.0236	0.1835	-0.0121	0.2052	-4.6302	11.8518	-13.1787
14	1.6328	0.0149	1.7309	0.9649	0.0468	7.8847	0.0314	-0.281	-0.1295	0.145	0.0287	0.0573	-0.0731	-0.1685	-0.0478	0.1512	-0.0187	0.0107	0.2019	0.0253	0.1513	-13.9624	-1.3094	-5.1493
15	7.8739	2.4105	0.7356	8.8857	-0.7343	8.5373	-0.2543	0.2927	0.8658	-0.1708	0.1914	0.4461	-1.0746	-0.3698	0.0254	0.3386	0.0541	-0.0185	0.2781	-0.0597	0.2985	-9.8714	16.9168	-5.2957
16	3.1218	3.3502	-3.5228	3.8031	-3.976	4.2644	0.1621	0.1335	0.5609	0.1312	-0.0791	0.7545	-0.5875	-1.1572	-0.0911	0.4717	0.139	0.0033	0.4668	-0.1108	0.408	-12.787	14.7412	1.4816
17	2.1397	0.3792	-0.973	2.288	-0.7893	5.9422	-0.0109	-0.2212	0.1963	0.3011	-0.05	-0.0103	-0.2341	0.0556	0.0336	0.2002	0.0091	0.0032	0.1513	-0.0451	0.1831	-3.0778	10.5043	-3.0055
18	7.1044	1.972	5.6574	3.6425	-0.5777	5.9996	0.2204	-0.7608	0.2166	0.1549	-0.0572	1.1834	-1.0973	-1.5905	-0.0851	0.3395	0.1891	0.011	0.7248	-0.021	0.4094	-18.0489	4.1624	6.7215
19	1.2437	-0.9365	0.3862	3.0024	0.4746	5.5392	0.0782	-0.2088	-0.3554	0.2413	-0.0989	0.1048	0.426	-0.3644	0.0355	0.2198	-0.0599	-0.0035	0.2343	0.0297	0.2024	-8.5931	-6.5927	-1.0058
20	2.9144	-0.2428	0.2717	3.9702	2.1602	7.8629	-0.0338	-0.5766	0.0381	0.6291	0.175	-0.3185	0.1956	0.3378	-0.1328	0.2653	0.0055	-0.0394	0.2964	-0.0127	0.1835	0.9946	1.5348	5.4526

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 18 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 56 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 57 through 74 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 75 through 101 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 102 through 112 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 113 through 125 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 126 through 155 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 156 through 174 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 175 through 218 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 15 through 31 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 32 through 46 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 47 through 56 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 57 through 74 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 75 through 101 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 102 through 112 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 113 through 125 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 126 through 155 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 156 through 174 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 175 through 195 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 196 through 217 )

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