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

ID or keywords:

Entry

Database: PDB / ID: 9dtc

Title

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ADP Ribose bound, orthrhombic form2)

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: 1.4 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, orthrhombic form2)
Authors: Mian, M.R. / Liu, L. / Lovell, S. / Buchko, G.W. / Battaile, K.P.

History

Deposition	Sep 30, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9dtc.cif.gz	188.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9dtc.ent.gz	146.9 KB	Display	PDB format
PDBx/mmJSON format	9dtc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dt/9dtc ftp://data.pdbj.org/pub/pdb/validation_reports/dt/9dtc	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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) #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)

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)
#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

51.4 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)	57.426, 79.749, 91.982
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-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.2 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 23% 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 AMP and 15 mM ADP-ribose. Electron density consistent with the alpha-D- ...Details: 23% 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 AMP and 15 mM ADP-ribose. Electron density consistent with the alpha-D-ribose form. Subunit B contains AMP and ADP-ribose in the active site and were refined with grouped occupancies. plate Liu-S-102, F8. Puck: PSL-1006, Cryo: 10% extra PEG 4000 added to the drop.

Crystal

Density Matthews: 2.13 Å³/Da / Density % sol: 42.2 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 23% 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 AMP and 15 mM ADP-ribose. Electron density consistent with the alpha-D- ...

-
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: 1.4→48.71 Å / Num. obs: 83201 / % possible obs: 99.5 % / Redundancy: 10.2 % / CC_1/2: 0.999 / R_merge(I) obs: 0.074 / R_pim(I) all: 0.024 / R_rim(I) all: 0.078 / Χ²: 1.02 / Net I/σ(I): 16.6 / Num. measured all: 848621
Reflection shell	Resolution: 1.4→1.42 Å / % possible obs: 100 % / Redundancy: 9.6 % / R_merge(I) obs: 1.407 / Num. measured all: 38864 / Num. unique obs: 4068 / CC_1/2: 0.594 / R_pim(I) all: 0.474 / R_rim(I) all: 1.488 / Χ²: 1.04 / Net I/σ(I) obs: 1.6

-
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: 1.4→48.71 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.6 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1881	4157	5.01 %
R_work	0.1623	-	-
obs	0.1636	83046	99.14 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.4→48.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3197	0	122	369	3688

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3487
X-RAY DIFFRACTION	f_angle_d	1.084	4770
X-RAY DIFFRACTION	f_dihedral_angle_d	18.287	1357
X-RAY DIFFRACTION	f_chiral_restr	0.081	533
X-RAY DIFFRACTION	f_plane_restr	0.011	607

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 (%)
1.4-1.42	0.3202	122	0.3125	2638	X-RAY DIFFRACTION	100
1.42-1.43	0.279	140	0.2634	2587	X-RAY DIFFRACTION	100
1.43-1.45	0.2849	136	0.2589	2641	X-RAY DIFFRACTION	100
1.45-1.47	0.2267	152	0.2292	2606	X-RAY DIFFRACTION	100
1.47-1.49	0.2392	130	0.2169	2608	X-RAY DIFFRACTION	100
1.49-1.51	0.2113	139	0.2092	2659	X-RAY DIFFRACTION	100
1.51-1.53	0.2499	133	0.1906	2606	X-RAY DIFFRACTION	100
1.53-1.55	0.2256	135	0.1976	2623	X-RAY DIFFRACTION	100
1.55-1.58	0.2151	135	0.1876	2598	X-RAY DIFFRACTION	100
1.58-1.6	0.2004	130	0.1789	2672	X-RAY DIFFRACTION	100
1.6-1.63	0.196	123	0.1769	2623	X-RAY DIFFRACTION	100
1.63-1.66	0.2219	155	0.1706	2617	X-RAY DIFFRACTION	100
1.66-1.69	0.2033	159	0.174	2644	X-RAY DIFFRACTION	100
1.69-1.73	0.2047	152	0.1716	2609	X-RAY DIFFRACTION	100
1.73-1.76	0.2149	121	0.1745	2630	X-RAY DIFFRACTION	100
1.76-1.8	0.1976	124	0.1706	2655	X-RAY DIFFRACTION	100
1.8-1.85	0.19	142	0.1652	2621	X-RAY DIFFRACTION	99
1.85-1.9	0.2164	150	0.1566	2617	X-RAY DIFFRACTION	99
1.9-1.96	0.1749	136	0.1498	2627	X-RAY DIFFRACTION	100
1.96-2.02	0.1845	142	0.1575	2627	X-RAY DIFFRACTION	100
2.02-2.09	0.1941	144	0.1536	2665	X-RAY DIFFRACTION	100
2.09-2.18	0.1644	141	0.1522	2627	X-RAY DIFFRACTION	99
2.18-2.27	0.1691	151	0.148	2619	X-RAY DIFFRACTION	99
2.27-2.39	0.1979	119	0.151	2679	X-RAY DIFFRACTION	99
2.39-2.54	0.1488	151	0.1477	2621	X-RAY DIFFRACTION	99
2.54-2.74	0.1691	146	0.1526	2636	X-RAY DIFFRACTION	98
2.74-3.02	0.188	123	0.1584	2647	X-RAY DIFFRACTION	98
3.02-3.45	0.1727	142	0.1603	2619	X-RAY DIFFRACTION	97
3.45-4.35	0.174	129	0.1423	2629	X-RAY DIFFRACTION	96
4.35-48.71	0.1891	155	0.1583	2639	X-RAY DIFFRACTION	93

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	1.7207	0.8457	-0.9377	0.4315	-0.5387	0.872	-0.3818	0.0319	-0.3486	-0.0527	0.1109	-0.2158	0.3257	0.0441	-0.2032	0.1704	0.0344	0.0118	0.1362	0.0616	0.2711	9.5151	-18.7135	23.8104
2	0.3868	0.2778	-0.2861	0.6909	-0.0299	0.3301	-0.0997	-0.1611	-0.0666	0.0843	-0.1181	-0.0564	0.1757	0.1574	-0.253	0.172	0.0287	-0.0068	0.206	0.1044	0.1834	2.4158	-15.9956	27.8523
3	0.3743	0.1345	-0.2022	0.1309	0.0388	0.1935	-0.0219	0.0941	-0.0299	-0.034	0.0082	0.0438	0.0083	-0.1085	-0.0003	0.1325	-0.0027	0.004	0.1343	0.0008	0.1136	-9.7927	-3.4839	6.8204
4	0.0957	-0.0116	0.0398	0.0488	0.06	0.0992	-0.0577	0.1021	-0.2035	-0.155	0.0922	0.0148	0.1607	-0.2503	0.0004	0.2237	-0.0508	0.0111	0.1679	-0.0212	0.2559	-8.9476	-16.6457	4.5454
5	0.2331	-0.1335	-0.0666	0.3639	-0.3176	0.4516	-0.0244	0.0638	-0.134	-0.0981	-0.0059	-0.016	0.1548	0.0488	-0.0382	0.1759	-0.0151	0.0124	0.1287	-0.0258	0.1359	-5.3756	-11.7507	1.3672
6	0.4929	0.1594	-0.4288	0.855	-0.0893	1.1246	-0.052	0.1975	-0.0157	-0.1057	0.0346	0.0334	-0.0207	-0.1235	-0.0001	0.1484	0.0019	0.0021	0.1831	-0.0002	0.1198	-6.8018	0.1008	-3.3748
7	0.6665	-0.3686	-0.0595	0.3268	0.2566	0.4061	-0.0392	0.0463	0.0598	0.0537	-0.047	0.0781	-0.0741	-0.0464	-0.0013	0.1362	0.0042	0.0012	0.165	0.019	0.1487	-22.1426	-1.5996	17.4991
8	0.3498	0.0523	0.0578	0.2776	0.0915	0.0677	-0.011	-0.0753	-0.0915	0.0205	0.0076	-0.0712	0.0135	0.0305	0	0.1289	0.0069	0.0041	0.1227	0.015	0.1403	5.8454	-4.2641	17.4975
9	0.1065	0.1545	0.0166	0.2157	0.0155	0.0144	0.124	-0.3036	0.061	0.0893	0.0366	0.0983	0.0041	0.0026	0.0002	0.1796	-0.0042	0.0405	0.209	-0.0107	0.1934	1.599	5.8595	25.3744
10	0.577	-0.002	-0.1617	0.2451	-0.0153	0.0329	0.0052	-0.0624	0.1365	-0.003	0.0206	0.0278	-0.0111	-0.0178	-0	0.1299	0.0012	0.0101	0.1263	-0.01	0.1365	4.6285	7.1807	19.0792
11	0.8829	0.2535	-0.0956	0.7953	0.147	0.5368	-0.0112	0.0078	-0.0078	-0.0175	0.0228	-0.0386	0.0155	0.0842	0	0.122	0.0032	0.007	0.1336	0.0022	0.1281	13.9316	2.034	11.9118

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 48 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 49 through 93 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 94 through 104 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 105 through 147 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 148 through 210 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 7 through 48 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 49 through 93 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 94 through 104 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 105 through 147 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 148 through 209 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi