PDB-9b21: Crystal structure of ADP-ribose diphosphatase from Klebsiella pne...

ID or keywords:

Entry

Database: PDB / ID: 9b21

Title

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ADP Ribose bound, Orthorhombic P form)

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: 1.6 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 (ADP Ribose bound, Orthorhombic P form)
Authors: Lovell, S. / Liu, L. / 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	9b21.cif.gz	186.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9b21.ent.gz	146 KB	Display	PDB format
PDBx/mmJSON format	9b21.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/b2/9b21 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/9b21	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	#213 - Sep 2017 Sirtuins similarity (1) #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

50.7 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)	57.365, 78.788, 91.564
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-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₅O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.09 Å³/Da / Density % sol: 41.17 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 26% PEG 4000, 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 ADP-ribose. Electron density consistent with the alpha-D-ribose form. ...Details: 26% PEG 4000, 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 ADP-ribose. Electron density consistent with the alpha-D-ribose form. plate Liu-S-102, D6. Puck: PSL-1005, Cryo: 33% PEG 4000.

Crystal

Density Matthews: 2.09 Å³/Da / Density % sol: 41.17 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 26% PEG 4000, 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 ADP-ribose. Electron density consistent with the alpha-D-ribose form. ...

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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: 1.6→48.61 Å / Num. obs: 55537 / % possible obs: 100 % / Redundancy: 13 % / CC_1/2: 0.999 / R_merge(I) obs: 0.107 / R_pim(I) all: 0.031 / R_rim(I) all: 0.111 / Net I/σ(I): 13
Reflection shell	Resolution: 1.6→1.64 Å / Redundancy: 12.8 % / R_merge(I) obs: 1.954 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4056 / CC_1/2: 0.629 / R_pim(I) all: 0.56 / R_rim(I) all: 2.035 / % possible all: 100

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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: 1.6→48.61 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.37 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1956	2799	5.05 %
R_work	0.1638	-	-
obs	0.1653	55464	99.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→48.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3212	0	76	273	3561

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3422
X-RAY DIFFRACTION	f_angle_d	1.01	4668
X-RAY DIFFRACTION	f_dihedral_angle_d	13.695	1371
X-RAY DIFFRACTION	f_chiral_restr	0.064	529
X-RAY DIFFRACTION	f_plane_restr	0.011	596

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 (%)
1.6-1.63	0.3365	158	0.2884	2574	X-RAY DIFFRACTION	100
1.63-1.66	0.276	127	0.2592	2615	X-RAY DIFFRACTION	100
1.66-1.69	0.2427	138	0.2226	2600	X-RAY DIFFRACTION	100
1.69-1.72	0.2756	154	0.2171	2559	X-RAY DIFFRACTION	100
1.72-1.76	0.2241	138	0.2108	2609	X-RAY DIFFRACTION	100
1.76-1.8	0.2223	137	0.1981	2631	X-RAY DIFFRACTION	100
1.8-1.85	0.2232	148	0.1909	2560	X-RAY DIFFRACTION	100
1.85-1.9	0.2183	116	0.1879	2626	X-RAY DIFFRACTION	100
1.9-1.95	0.2431	119	0.1766	2644	X-RAY DIFFRACTION	100
1.95-2.02	0.1945	137	0.1699	2613	X-RAY DIFFRACTION	100
2.02-2.09	0.1931	143	0.1615	2602	X-RAY DIFFRACTION	100
2.09-2.17	0.2042	144	0.1511	2621	X-RAY DIFFRACTION	100
2.17-2.27	0.1992	160	0.1555	2604	X-RAY DIFFRACTION	100
2.27-2.39	0.2041	142	0.1575	2646	X-RAY DIFFRACTION	100
2.39-2.54	0.2053	130	0.1575	2630	X-RAY DIFFRACTION	100
2.54-2.74	0.2085	140	0.1585	2659	X-RAY DIFFRACTION	100
2.74-3.01	0.1714	138	0.1675	2646	X-RAY DIFFRACTION	100
3.01-3.45	0.1948	143	0.165	2676	X-RAY DIFFRACTION	100
3.45-4.34	0.1656	131	0.1337	2722	X-RAY DIFFRACTION	100
4.34-48.61	0.1703	156	0.1555	2828	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	7.0714	2.2706	-2.397	3.4981	-1.1126	2.0081	-0.5113	-0.1498	-0.804	-0.0511	0.0549	-0.5914	0.3861	0.1255	0.5241	0.2597	0.0301	0.0119	0.1738	0.0186	0.2741	9.665	-18.963	23.687
2	7.5989	0.9804	-0.6028	1.7921	-0.9719	1.4753	0.0862	-0.7299	-0.465	0.14	-0.1393	-0.152	0.1515	0.1818	-0.0121	0.2286	0.0397	-0.0005	0.1912	0.0306	0.1982	2.816	-16.032	27.938
3	0.9406	0.1299	-0.4296	0.5257	0.0713	1.6571	-0.0045	0.1758	0.0275	-0.0658	-0.013	0.0607	-0.0814	-0.1258	0.0144	0.1351	-0.0195	0.007	0.1526	-0.0049	0.1382	-9.877	-3.459	7.372
4	8.3723	-5.4033	4.3967	7.9422	-0.3292	8.1427	0.13	-0.3772	-0.6678	-0.1603	0.242	0.2092	0.7156	-0.444	-0.35	0.2495	-0.0906	0.0258	0.2161	-0.0133	0.2579	-10.617	-15.589	1.029
5	1.3099	-0.3204	0.9385	0.7617	-0.6965	4.8319	-0.0598	0.258	-0.1149	-0.1709	-0.0274	0.0351	0.2522	0.0757	0.074	0.1868	-0.0338	0.0073	0.1776	-0.0246	0.1658	-3.803	-9.562	0.514
6	5.4405	1.7801	-0.0599	3.4171	0.429	4.2222	-0.0159	0.3899	-0.0661	0.0107	0.0322	0.1525	0.0261	-0.3631	-0.0131	0.1534	0.0577	0.008	0.2282	0.0038	0.1498	-13.104	1.386	0.063
7	2.7893	0.1429	-1.4614	2.9821	1.5484	2.0229	-0.0416	0.2654	-0.081	-0.4025	0.0432	-0.1603	-0.1395	0.2831	-0.0259	0.1829	0.009	0.0189	0.2271	0.0107	0.1252	2.099	-1.627	-7.116
8	5.9119	-0.9793	-0.1321	6.8539	-3.7752	4.6759	0.0861	0.0655	0.2828	0.0894	0.0594	0.3545	-0.1539	0.1023	-0.1748	0.1521	0.011	-0.0264	0.1984	-0.0468	0.2099	-23.329	2.7	15.988
9	5.084	-3.4426	5.0541	2.7852	-3.1427	6.7996	-0.1793	-0.2913	-0.0907	0.2251	0.1946	0.1293	-0.0261	-0.1361	-0.0089	0.1967	-0.0058	0.0304	0.1891	-0.0008	0.1484	-17.373	-5.886	24.556
10	5.7078	2.9089	-4.626	8.7664	-2.08	3.8448	0.206	-0.0726	0.005	0.0621	-0.1453	0.4844	-0.3081	-0.3785	-0.0414	0.1269	0.0397	-0.037	0.3081	-0.005	0.2164	-29.572	-1.629	8.06
11	2.3279	0.2869	0.0962	0.6119	0.2126	0.1664	0.0271	-0.0088	0.0199	0.0117	0.03	-0.0372	0.0227	0.0013	-0.0521	0.173	0.0074	-0.009	0.1531	-0.0034	0.1319	5.44	0.754	16.738
12	6.3312	3.4465	-0.0905	3.9887	-0.3742	3.4691	-0.0811	-0.1945	-0.2059	0.2418	0.0487	-0.016	0.0386	0.2133	0.0064	0.1453	0.0331	0.0034	0.1487	0.0129	0.1672	7.885	-12.511	18.037
13	5.6945	-3.3683	0.4764	7.3684	2.032	3.1637	0.1065	-0.6996	0.0845	0.1888	0.0498	0.2156	-0.126	-0.0765	-0.1442	0.211	-0.0172	0.0362	0.253	-0.008	0.1771	5.257	7.005	25.757
14	7.5535	4.174	-0.4099	3.1473	-0.31	0.0294	-0.1158	0.109	0.2317	-0.0863	0.1695	0.0292	-0.0073	0.009	-0.0618	0.1386	0.0049	0.0133	0.1414	-0.0251	0.1098	2.525	6.504	15.709
15	3.5528	1.4468	1.4501	5.881	-2.7779	4.2171	0.2979	-0.5243	-0.1787	0.8572	-0.2566	-0.1269	-0.1968	0.1612	-0.1455	0.2978	0.011	0.0302	0.2762	-0.0466	0.206	17.092	0.107	25.754
16	3.1995	1.1024	0.1325	2.7184	-0.3683	2.1685	-0.0511	0.1426	0.0856	-0.2328	0.0838	-0.0847	0.0315	0.1295	-0.0325	0.1224	0.0072	0.0128	0.1656	-0.0103	0.1283	12.891	2.893	6.907

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 7:23 )	A	7 - 23
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 24:48 )	A	24 - 48
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 49:93 )	A	49 - 93
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 94:117 )	A	94 - 117
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 118:152 )	A	118 - 152
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 153:187 )	A	153 - 187
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 188:210 )	A	188 - 210
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 8:23 )	B	8 - 23
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 24:38 )	B	24 - 38
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 39:48 )	B	39 - 48
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 49:78 )	B	49 - 78
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 79:94 )	B	79 - 94
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 95:117 )	B	95 - 117
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 118:147 )	B	118 - 147
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 148:166 )	B	148 - 166
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 167:209 )	B	167 - 209

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