PDB-4nbq: Structure of the polynucleotide phosphorylase (CBU_0852) from Cox...

ID or keywords:

Entry

Database: PDB / ID: 4nbq

Title

Structure of the polynucleotide phosphorylase (CBU_0852) from Coxiella burnetii

Components

Polyribonucleotide nucleotidyltransferase

Keywords

TRANSFERASE / Phosphorylase

Function / homology

Function and homology information

polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / RNA catabolic process / mRNA catabolic process / RNA processing / 3'-5'-RNA exonuclease activity / magnesium ion binding / RNA binding / cytosol
Similarity search - Function

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.9138 Å

Authors

Rudolph, M.J. / Cheung, J. / Franklin, M.C. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.

Citation

Journal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.

History

Deposition	Oct 23, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 17, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	Jan 20, 2016	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4nbq.cif.gz	755.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4nbq.ent.gz	631 KB	Display	PDB format
PDBx/mmJSON format	4nbq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4nbq_validation.pdf.gz	489.5 KB	Display	wwPDB validaton report
Full document	4nbq_full_validation.pdf.gz	572.2 KB	Display
Data in XML	4nbq_validation.xml.gz	74.8 KB	Display
Data in CIF	4nbq_validation.cif.gz	99.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nb/4nbq ftp://data.pdbj.org/pub/pdb/validation_reports/nb/4nbq	HTTPS FTP

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Related structure data

Related structure data	3tq8C 3tq9C 3tqaC 3tqbC 3tqcC 3tqdC 3tqeC 3tqfC 3tqgC 3tqhC 3tqiC 3tqjC 3tqlC 3tqmC 3tqnC 3tqoC 3tqpC 3tqqC 3tqrC 3tqsC 3tqtC 3tquC 3tqwC 3tqxC 3tqyC 3tqzC 3tr0C 3tr1C 3tr2C 3tr3C 3tr4C 3tr5C 3tr6C 3tr7C 3tr8C 3tr9C 3trbC 3trcC 3trdC 3treC 3trfC 3trgC 3trhC 3triC 3tthC 3ty2C 3uwcC 4f3qC 4f3rC 4ng4C 3cdiS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1v0e-1 2495 1v0f-2 7cg0-d 3lee-d 1v0f-1 7a5v-1 3ju4-1 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	#86 - Feb 2007 Exosomes similarity (9) #253 - Jan 2021 Expressome similarity (4) #255 - Mar 2021 Cisplatin and DNA similarity (3) #241 - Jan 2020 Twenty Years of Molecules similarity (3)

Deposited unit

A: Polyribonucleotide nucleotidyltransferase

B: Polyribonucleotide nucleotidyltransferase

C: Polyribonucleotide nucleotidyltransferase

hetero molecules

240 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	99.710, 111.358, 219.062
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Polyribonucleotide nucleotidyltransferase / Polynucleotide phosphorylase / PNPase Mass: 79690.078 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 / Nine Mile phase I / Gene: pnp, CBU_0852 / Production host: Escherichia coli (E. coli) References: UniProt: Q83D87, polyribonucleotide nucleotidyltransferase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.64 Å³/Da / Density % sol: 53.42 %
Crystal grow	Method: vapor diffusion / Details: VAPOR DIFFUSION

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 0.9792 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 29, 2012

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 2.9→50 Å / Num. all: 53776 / Num. obs: 51088 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / R_merge(I) obs: 0.097 / Net I/σ(I): 8.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.9-2.95	5	0.518	1	88.9
2.95-3	5	0.455	1	88.1
3-3.06	5	0.398	1	88.3
3.06-3.12	5	0.314	1	88.3
3.12-3.19	4.9	0.28	1	88.6
3.19-3.27	4.9	0.23	1	89.5
3.27-3.35	4.9	0.189	1	91.1
3.35-3.44	4.8	0.171	1	92.8
3.44-3.54	4.8	0.139	1	94.5
3.54-3.65	4.7	0.12	1	96.7
3.65-3.78	4.7	0.108	1	98
3.78-3.94	4.7	0.097	1	98.5
3.94-4.11	4.8	0.089	1	98.8
4.11-4.33	4.9	0.08	1	99.4
4.33-4.6	5	0.073	1	99.4
4.6-4.96	5.2	0.078	1	99.8
4.96-5.46	5.5	0.086	1	99.9
5.46-6.24	5.6	0.088	1	99.8
6.24-7.86	5.4	0.08	1	99.2
7.86-50	5.2	0.071	1	98.6

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 32.51 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.91 Å	49.63 Å
Translation	2.91 Å	49.63 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER	2.1.4	phasing
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CDI

3cdi

Resolution: 2.9138→49.634 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.79 / σ(F): 1.37 / Phase error: 25.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2595	2590	5.08 %
R_work	0.2083	-	-
obs	0.2109	51021	94.34 %

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 50.751 Å² / k_sol: 0.334 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.617 Å²	0 Å²	-0 Å²
2-	-	-2.0981 Å²	-0 Å²
3-	-	-	-2.5189 Å²

Refinement step

Cycle: LAST / Resolution: 2.9138→49.634 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14840	0	65	12	14917

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	15110
X-RAY DIFFRACTION	f_angle_d	0.998	20413
X-RAY DIFFRACTION	f_dihedral_angle_d	15.508	5693
X-RAY DIFFRACTION	f_chiral_restr	0.07	2367
X-RAY DIFFRACTION	f_plane_restr	0.003	2649

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 (%)
2.9138-2.9699	0.3232	105	0.2552	2249	X-RAY DIFFRACTION	80
2.9699-3.0305	0.3351	133	0.2496	2475	X-RAY DIFFRACTION	88
3.0305-3.0964	0.3198	133	0.2482	2495	X-RAY DIFFRACTION	88
3.0964-3.1684	0.3122	125	0.2409	2496	X-RAY DIFFRACTION	88
3.1684-3.2476	0.2998	145	0.2378	2469	X-RAY DIFFRACTION	89
3.2476-3.3354	0.3184	147	0.2352	2515	X-RAY DIFFRACTION	90
3.3354-3.4335	0.2843	124	0.2222	2614	X-RAY DIFFRACTION	92
3.4335-3.5443	0.2673	135	0.2061	2663	X-RAY DIFFRACTION	94
3.5443-3.671	0.2504	145	0.209	2728	X-RAY DIFFRACTION	96
3.671-3.8179	0.2685	157	0.2067	2764	X-RAY DIFFRACTION	98
3.8179-3.9916	0.2552	166	0.1944	2788	X-RAY DIFFRACTION	99
3.9916-4.2019	0.2268	150	0.1784	2797	X-RAY DIFFRACTION	99
4.2019-4.465	0.2147	158	0.1635	2841	X-RAY DIFFRACTION	100
4.465-4.8095	0.1936	157	0.1594	2841	X-RAY DIFFRACTION	99
4.8095-5.293	0.2218	143	0.1911	2880	X-RAY DIFFRACTION	100
5.293-6.0578	0.2767	140	0.2386	2882	X-RAY DIFFRACTION	100
6.0578-7.6277	0.2725	174	0.2169	2908	X-RAY DIFFRACTION	99
7.6277-49.6413	0.2814	153	0.2337	3026	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	3.7108	0.54	0.0996	2.2405	-0.4469	3.7297	-0.0497	-0.0535	0.0683	0.1387	0.0425	-0.5112	0.1159	0.5132	0.0202	0.2618	0.0595	-0.0091	0.2596	-0.0622	0.3998	23.2662	-8.2993	46.5801
2	2.6079	-0.2006	0.6895	1.8867	0.063	2.7199	-0.0732	-0.0576	0.209	0.0183	0.0422	-0.1747	0.041	0.1616	-0.0069	0.2198	0.0292	0.0164	0.1696	-0.0295	0.2646	10.8502	-8.3971	45.5409
3	3.2231	-1.5114	0.0505	6.2335	2.9286	4.0477	-0.1897	-0.1433	0.0928	-0.1821	-0.0958	0.2446	0.0678	-0.4124	0.1783	0.4188	-0.004	0.0929	0.1732	-0.0142	0.3383	-5.1817	22.0341	67.3528
4	0.9427	-0.0726	0.0405	1.5074	0.1153	3.1146	-0.1085	-0.0457	-0.1007	-0.0369	0.1966	-0.0533	0.1114	0.3935	-0.0969	0.2636	0.0214	-0.0148	0.228	0.0114	0.1583	-2.0312	10.8844	41.8274
5	1.864	0.0241	-1.4438	1.4804	0.209	3.3326	-0.0137	0.1215	-0.1562	-0.1196	0.0047	-0.1219	0.1011	0.2336	-0.0247	0.1514	0.0344	-0.0825	0.2033	-0.0021	0.1977	-3.2849	2.5987	30.4343
6	3.6254	0.481	-3.4192	0.9582	-1.6975	4.7869	-0.392	0.306	-0.175	-0.1587	-0.0878	-0.4347	0.0895	-0.093	0.059	0.9569	-0.1836	0.2088	0.8376	-0.1587	0.5271	14.8459	3.2804	-16.4353
7	2.5404	0.269	-0.8452	3.821	0.155	2.117	-0.0916	0.1811	0.1408	-0.7629	0.1211	0.0352	-0.2463	-0.1416	-0.0516	0.4596	-0.0213	-0.0345	0.1795	0.0307	0.1288	5.1346	33.4417	21.4102
8	0.8181	-0.3203	-0.123	1.6443	0.993	1.7313	-0.1519	0.1339	0.1035	-0.5891	0.0104	-0.4486	0.1131	0.0496	0.0711	0.5785	-0.1048	0.2577	0.4199	0.0455	0.5151	27.878	42.2807	23.4781
9	-0.4446	-0.4091	-0.5554	2.7484	2.3029	1.45	0.091	-0.1613	0.127	0.2535	-0.0723	0.2982	0.435	0.1568	-0.0742	1.0036	0.1299	0.2656	0.8758	-0.0214	0.5426	40.2256	-2.3175	-10.3498
10	1.1011	-0.1158	0.886	1.8839	-0.0754	2.0124	-0.1394	-0.1045	-0.0123	-0.0219	0.1641	-0.6369	-0.4338	0.0611	-0.0595	0.2048	-0.0382	0.3257	0.5887	-0.0878	0.9063	50.4693	19.2776	39.176
11	2.021	0.3136	0.9631	1.6422	0.1066	2.0021	0	0.2711	0.0664	-0.4782	0.0095	-0.4694	-0.0353	0.2454	-0.0057	0.3139	0.0512	0.2082	0.4496	-0.036	0.6688	42.5666	-6.5429	31.6222

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 0:74)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 75:238)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 239:284)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 285:378)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 379:576)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 577:692)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 0:225)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 226:541)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 542:692)
10	X-RAY DIFFRACTION	10	chain 'C' and (resseq 1:313)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 314:619)

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