PDB-9b20: Crystal structure of ADP-ribose diphosphatase from Klebsiella pne...

ID or keywords:

Entry

Database: PDB / ID: 9b20

Title

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (AMP 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-ribose diphosphatase /

ADP-ribose diphosphatase activity /

metal ion binding
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 (AMP bound)
Authors: Liu, L. / Lovell, S. / Buchko, G.W. / Battaile, K.P.

History

Deposition	Mar 14, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9b20.cif.gz	179.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9b20.ent.gz	140.3 KB	Display	PDB format
PDBx/mmJSON format	9b20.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/b2/9b20 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/9b20	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) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: ADP-ribose pyrophosphatase

B: ADP-ribose pyrophosphatase

hetero molecules

50.3 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)	49.910, 68.790, 56.663
Angle α, β, γ (deg.)	90.00, 115.20, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 326 / 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: 1.78 Å³/Da / Density % sol: 30.84 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 33% Peg 3350, 0.1M Tris, pH 8.5, 0.2 M sodium acetate, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. 3 minutue soak in 15 mM AMP. plate Liu-S-102, C1. Puck: PSL-1003, Cryo: direct.

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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: Feb 10, 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→45.16 Å / Num. obs: 48638 / % possible obs: 96.8 % / Redundancy: 6.9 % / CC_1/2: 0.986 / R_merge(I) obs: 0.175 / R_pim(I) all: 0.072 / R_rim(I) all: 0.19 / Χ²: 0.96 / Net I/σ(I): 7.8 / Num. measured all: 337486
Reflection shell	Resolution: 1.55→1.59 Å / % possible obs: 95.2 % / Redundancy: 7.1 % / R_merge(I) obs: 1.334 / Num. measured all: 24961 / Num. unique obs: 3505 / CC_1/2: 0.611 / R_pim(I) all: 0.536 / R_rim(I) all: 1.439 / Χ²: 0.89 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	(dev_5243: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.55→45.16 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2032	2435	5.01 %
R_work	0.164	-	-
obs	0.166	48574	96.5 %

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→45.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3125	0	49	326	3500

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3296
X-RAY DIFFRACTION	f_angle_d	1.024	4493
X-RAY DIFFRACTION	f_dihedral_angle_d	13.837	1218
X-RAY DIFFRACTION	f_chiral_restr	0.059	503
X-RAY DIFFRACTION	f_plane_restr	0.011	580

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 (%)
1.55-1.58	0.3273	144	0.2805	2621	X-RAY DIFFRACTION	95
1.58-1.62	0.2937	129	0.2564	2705	X-RAY DIFFRACTION	95
1.62-1.65	0.2843	162	0.222	2637	X-RAY DIFFRACTION	96
1.65-1.69	0.2322	122	0.2027	2710	X-RAY DIFFRACTION	96
1.7-1.74	0.2487	142	0.1915	2668	X-RAY DIFFRACTION	96
1.74-1.79	0.2297	180	0.1817	2678	X-RAY DIFFRACTION	96
1.79-1.85	0.2136	140	0.1704	2705	X-RAY DIFFRACTION	96
1.85-1.92	0.189	154	0.1589	2676	X-RAY DIFFRACTION	96
1.92-1.99	0.2023	142	0.1569	2722	X-RAY DIFFRACTION	97
1.99-2.08	0.172	124	0.1447	2731	X-RAY DIFFRACTION	97
2.08-2.19	0.2051	100	0.1393	2740	X-RAY DIFFRACTION	97
2.19-2.33	0.1886	135	0.1481	2735	X-RAY DIFFRACTION	97
2.33-2.51	0.2002	127	0.1524	2778	X-RAY DIFFRACTION	98
2.51-2.76	0.1976	139	0.1606	2765	X-RAY DIFFRACTION	98
2.76-3.16	0.1872	138	0.1655	2756	X-RAY DIFFRACTION	97
3.16-3.98	0.1867	200	0.1543	2669	X-RAY DIFFRACTION	97
3.98-45.16	0.2022	157	0.1609	2843	X-RAY DIFFRACTION	99

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	0.0553	0.0627	0.0054	0.1605	0.0943	0.1306	-0.0944	0.1417	-0.0565	0.0098	0.1173	-0.0272	0.1152	-0.0408	-0.0021	0.1897	-0.0577	0.0045	0.2446	-0.0112	0.1546	-1.6739	16.8398	7.206
2	0.1823	0.1543	0.0162	0.1716	0.091	0.0306	0.0905	-0.0094	0.1358	-0.0536	0.1663	-0.1226	-0.1985	0.097	0.0032	0.1727	-0.0196	0.0075	0.199	-0.0046	0.1612	7.1087	13.938	-3.819
3	0.7867	-1.1188	-0.6262	1.6113	0.8572	0.7683	0.166	-0.01	0.1507	-0.1049	0.0062	-0.1426	0.2411	-0.0093	0.252	0.1676	-0.0176	-0.0262	0.1897	0.0328	0.1336	-0.8615	10.2613	14.9118
4	0.0608	-0.234	-0.1046	0.0772	-0.0395	0.1579	0.0079	0.069	-0.0163	-0.036	-0.0261	-0.0192	-0.0155	0.018	0	0.1363	-0.0006	-0.0051	0.1369	-0.0014	0.1464	-10.3541	10.9749	-20.2906
5	0.1076	0.0004	0.0555	0.1877	-0.0845	0.099	0.0589	0.1968	0.1829	-0.1579	-0.0501	-0.2795	-0.0586	0.3446	-0.0002	0.1677	0.0021	0.0009	0.2102	0.0084	0.2227	-10.0704	25.1748	-20.5934
6	0.1388	-0.1303	0.1709	0.1777	0.0527	0.138	-0.0334	-0.0634	0.0186	0.0039	0.0259	0.0029	-0.0367	-0.0437	0.0003	0.1193	-0.0019	-0.0065	0.1248	0.0131	0.1265	-15.0497	18.8681	-14.1156
7	-0.0009	0.003	-0.0035	0.0261	0.047	0.0122	-0.0984	0.3475	0.2612	-0.2883	0.0034	-0.2096	-0.0013	-0.1433	0.0004	0.3036	0.0177	0.0083	0.2584	0.0047	0.2281	-17.4243	19.558	-32.448
8	0.5455	0.1295	0.1812	0.6285	-0.4024	0.3337	0.0291	-0.0127	-0.1274	0.0106	0.0252	0.1904	0.0917	-0.0662	0.0017	0.1239	0.0052	-0.0093	0.1484	0.003	0.1367	-24.4058	10.8342	-20.2544
9	0.0726	0.0856	0.0046	0.254	0.0569	0.437	0.0197	-0.1117	0.0853	0.1027	0.0011	0.0573	0.2588	0.0121	0.019	0.1257	0.0124	-0.0211	0.1537	-0.0171	0.1435	2.5252	1.6481	-29.3929
10	0.3116	-0.3167	-0.0765	0.2918	0.3298	0.3842	-0.0822	-0.0004	-0.0323	0.0587	0.1458	-0.0859	-0.2361	0.1459	0.0138	0.1648	-0.0131	-0.0202	0.1934	0.0115	0.1711	4.6496	6.7378	-25.1234
11	0.1299	0.0875	-0.0083	0.1993	-0.0811	0.1521	-0.0338	-0.0064	-0.0167	-0.0161	0.018	0.0209	0.0562	0.0001	-0.0001	0.1505	-0.0004	-0.0131	0.146	0.0048	0.1449	-11.606	2.7813	-4.2265
12	0.1205	-0.0778	-0.1803	0.0519	0.0914	0.201	0.0006	-0.0098	-0.0584	-0.0675	0.0708	-0.1309	0.0642	0.0593	-0.0002	0.1359	-0.0036	-0.0166	0.1312	-0.006	0.166	-7.4941	13.6637	1.7528
13	0.0201	-0.0041	-0.0352	0.0337	0.0316	0.2049	-0.0194	-0.0874	0.1154	0.226	-0.0134	-0.0746	0.2746	-0.1423	0.0007	0.1742	0.0457	-0.0104	0.1695	-0.0074	0.1921	-4.0982	-6.3791	-4.9473
14	0.2687	-0.1975	-0.4591	0.2262	0.3583	0.8267	-0.2241	-0.236	0.0757	0.1904	0.1346	-0.011	0.4971	0.3145	-0.0113	0.2364	0.0465	-0.0018	0.1777	-0.0069	0.1597	-10.2695	-7.702	0.9159
15	0.1822	-0.0957	-0.2745	0.231	0.144	0.2413	-0.0735	0.0829	-0.07	0.026	0.0458	-0.0196	0.1698	-0.0428	0.0004	0.1632	-0.0032	-0.0019	0.1374	0.0098	0.1369	-13.9863	-2.1046	-8.1805
16	0.4474	0.1044	-0.1748	1.1475	-0.3181	0.5914	-0.0061	-0.0621	-0.0086	0.0264	0.0498	0.0205	-0.0021	0.0274	-0	0.1163	-0.0035	-0.0031	0.1441	0.0102	0.1432	-20.723	3.6442	1.0103

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 48 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 49 through 94 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 95 through 117 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 118 through 147 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 148 through 166 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 167 through 210 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 10 through 23 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 24 through 48 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 49 through 78 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 79 through 94 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 95 through 104 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 105 through 117 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 118 through 147 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 148 through 209 )

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