PDB-6vr4: Virion-packaged DNA-dependent RNA polymerase of crAss-like phage ...

ID or keywords:

Entry

Database: PDB / ID: 6vr4

Title

Virion-packaged DNA-dependent RNA polymerase of crAss-like phage phi14:2

Components

DNA-dependent RNA polymerase

Keywords

VIRAL PROTEIN / TRANSFERASE / TRANSCRIPTION / DNA-dependent RNA polymerase / RNAP / RNApol

Function / homology

Structural protein

Function and homology information

Biological species

Cellulophaga phage phi14:2 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.5 Å

Authors

Leiman, P.G. / Sokolova, M.L.

Citation

Journal: Nature / Year: 2020
Title: Structure and function of virion RNA polymerase of a crAss-like phage.
Authors: Drobysheva, A.V. / Panafidina, S.A. / Kolesnik, M.V. / Klimuk, E.I. / Minakhin, L. / Yakunina, M.V. / Borukhov, S. / Nilsson, E. / Holmfeldt, K. / Yutin, N. / Makarova, K.S. / Koonin, E.V. / ...

History

Deposition	Feb 6, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	Dec 2, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Dec 9, 2020	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	Jan 20, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6vr4.cif.gz	1.7 MB	Display	PDBx/mmCIF format
PDB format	pdb6vr4.ent.gz	1.5 MB	Display	PDB format
PDBx/mmJSON format	6vr4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6vr4_validation.pdf.gz	463.1 KB	Display	wwPDB validaton report
Full document	6vr4_full_validation.pdf.gz	517.8 KB	Display
Data in XML	6vr4_validation.xml.gz	141.9 KB	Display
Data in CIF	6vr4_validation.cif.gz	190.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vr/6vr4 ftp://data.pdbj.org/pub/pdb/validation_reports/vr/6vr4	HTTPS FTP

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Related structure data

Similar structure data	3vst-d 2jj1-1 6hjx-d 1ohh-d 6ytf-d 0814 3vsu-d 2jj1-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: DNA-dependent RNA polymerase

B: DNA-dependent RNA polymerase

hetero molecules

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

1

A: DNA-dependent RNA polymerase

hetero molecules

defined by author
Evidence: gel filtration
252 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DNA-dependent RNA polymerase

hetero molecules

defined by author
252 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	266.441, 297.181, 92.015
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain A	A	2 - 2167
2	1	1	chain B	B	2 - 2167

#1: Protein	DNA-dependent RNA polymerase Mass: 251177.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellulophaga phage phi14:2 (virus) / Gene: Phi14:2_gp077 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S0A2C3
#2: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
Has ligand of interest	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: 3.65 Å³/Da / Density % sol: 66.32 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris-HCl, pH 8.5, 200 mM sodium acetate, 11% PEG4000, 2 mM TCEP

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 1, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 3.5→31.93 Å / Num. obs: 177687 / % possible obs: 99.7 % / Redundancy: 7.887 % / B_iso Wilson estimate: 72.599 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.176 / R_rim(I) all: 0.189 / Χ²: 1.024 / Net I/σ(I): 11.9 / Num. measured all: 1401490

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
3.5-3.71	7.897	0.942	2.25	225207	28684	28518	0.738	1.007	99.4
3.71-3.97	7.926	0.543	3.91	213737	27018	26965	0.891	0.581	99.8
3.97-4.28	7.926	0.327	6.43	197745	25023	24948	0.96	0.35	99.7
4.28-4.69	7.909	0.205	10.2	182856	23164	23121	0.983	0.22	99.8
4.69-5.23	7.911	0.169	12.07	165370	20924	20903	0.989	0.181	99.9
5.23-6.03	7.913	0.168	12.18	146342	18505	18494	0.988	0.179	99.9
6.03-7.36	7.891	0.119	16.97	123297	15633	15625	0.994	0.128	99.9
7.36-10.3	7.813	0.047	37.42	95196	12189	12185	0.999	0.05	100
10.3-31.93	7.468	0.031	50.4	51740	7004	6928	0.999	0.033	98.9

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Processing

Software

Name	Version	Classification
PHENIX	1.18.1_3865	refinement
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.5→31.93 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 24.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2394	8910	5.03 %
R_work	0.1919	168301	-
obs	0.1943	177211	99.65 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 464.25 Å² / B_iso mean: 93.0518 Å² / B_iso min: 39.62 Å²

Refinement step

Cycle: final / Resolution: 3.5→31.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	34688	0	27	0	34715
B_iso mean	-	-	77.69	-	-
Num. residues	-	-	-	-	4332

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	12658	X-RAY DIFFRACTION	2.731	TORSIONAL
1	2	B	12658	X-RAY DIFFRACTION	2.731	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.5-3.54	0.3178	292	0.3012	5576	5868	98
3.54-3.58	0.3473	290	0.2848	5594	5884	100
3.58-3.62	0.3013	299	0.2776	5643	5942	100
3.62-3.67	0.3243	298	0.2664	5630	5928	100
3.67-3.72	0.301	297	0.2581	5579	5876	99
3.72-3.77	0.2912	295	0.2442	5553	5848	100
3.77-3.82	0.313	301	0.2424	5729	6030	100
3.82-3.88	0.2817	289	0.2277	5526	5815	99
3.88-3.94	0.2577	301	0.2243	5619	5920	100
3.94-4	0.2695	302	0.2189	5663	5965	99
4-4.07	0.2525	291	0.2098	5535	5826	100
4.07-4.15	0.2786	301	0.2014	5716	6017	100
4.15-4.23	0.2503	293	0.1844	5559	5852	99
4.23-4.31	0.2314	295	0.1784	5637	5932	100
4.31-4.41	0.2287	297	0.1802	5610	5907	100
4.41-4.51	0.2239	294	0.164	5604	5898	100
4.51-4.62	0.2101	302	0.1597	5660	5962	100
4.62-4.75	0.2321	291	0.1592	5558	5849	100
4.75-4.89	0.2039	298	0.1598	5648	5946	100
4.89-5.04	0.2203	298	0.1585	5625	5923	100
5.04-5.22	0.1927	304	0.1688	5631	5935	100
5.22-5.43	0.2138	299	0.1766	5638	5937	100
5.43-5.68	0.2754	299	0.1905	5593	5892	100
5.68-5.97	0.2506	294	0.194	5625	5919	100
5.97-6.34	0.236	296	0.1988	5620	5916	100
6.35-6.83	0.2543	301	0.1994	5625	5926	100
6.83-7.51	0.2463	302	0.1854	5636	5938	100
7.51-8.58	0.1964	295	0.1614	5633	5928	100
8.58-10.74	0.1634	296	0.1427	5589	5885	100
10.74-31.93	0.2342	300	0.205	5447	5747	97

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	0.3391	0.2092	-0.1191	0.1179	-0.1159	0.2842	-0.0702	0.1248	-0.1462	-0.5001	-0.0098	0.1575	-0.1839	-0.0512	-0	1.0438	0.0334	-0.1237	0.8074	-0.0619	1.0125	172.9993	72.1455	44.7208
2	1.1406	0.6114	-0.3454	0.5993	0.3883	1.3615	0.0526	-0.1144	-0.0409	0.0946	-0.1977	0.1654	-0.0323	-0.0983	0	0.7873	0.0698	0.0135	0.7982	0.1067	0.8223	175.3447	88.6918	84.0739
3	1.0153	0.0101	0.0513	0.794	0.0739	0.9533	-0.0019	-0.2384	-0.0758	0.163	0.0011	-0.0203	-0.1718	0.2114	0	0.6475	0.0304	-0.0231	0.6558	0.0681	0.4698	201.0039	112.8016	80.2601
4	0.7408	-0.0239	-0.2106	0.1966	-0.1335	0.5745	0.059	0.1908	-0.1217	-0.1867	-0.0587	-0.0386	0.0113	0.0525	-0	0.6901	0.0987	0.0238	0.8344	-0.0086	0.6243	214.696	103.0943	49.2711
5	0.8044	-0.1702	-0.0376	0.9272	0.0588	0.7883	-0.0863	0.0496	0.0946	-0.1523	0.0322	0.0113	-0.1018	0.1701	0.0001	0.7616	0.016	-0.0078	0.7747	0.0867	0.6265	199.3218	123.2183	56.1404
6	0.6784	-0.0853	0.2957	0.9049	0.0104	0.5147	-0.0405	0.0294	-0.0478	-0.072	0.0745	0.3843	-0.059	0.0233	-0	0.6713	0.0655	-0.0623	0.6295	0.0308	0.7557	166.5153	117.3513	54.2001
7	0.603	0.2646	0.0932	0.1116	-0.0352	0.4791	0.1009	-0.4635	0.1818	-0.0588	0.0442	0.2191	0.0359	0.0608	0.0001	0.788	0.0305	0.0585	1.0049	0.0786	0.9736	198.0766	42.8922	81.9459
8	1.2631	-0.0207	-0.624	0.0663	0.1294	0.9183	-0.0345	0.1704	-0.0649	0.0271	0.0702	0.1235	0.1298	-0.0371	-0	0.6548	0.0546	-0.1522	0.6958	0.0473	0.8332	213.0673	37.651	42.8744
9	0.6388	0.1047	-0.0276	0.6403	0.1064	0.6344	0.0386	0.0681	0.0942	-0.0934	0.0596	-0.0056	-0.0204	0.1169	0	0.5053	0.0414	-0.1123	0.4978	-0.0174	0.5133	246.4512	49.1722	47.5245
10	0.4206	0.1706	0.2065	0.4166	-0.3639	0.6706	0.0052	-0.3385	0.3188	0.1985	0.1439	0.0007	-0.0301	-0.1471	0.0001	0.5556	0.0493	-0.0629	0.6906	-0.1628	0.6376	245.0327	68.3547	79.5607
11	0.2125	0.1564	0.0992	1.0877	-0.1136	0.4775	-0.0166	-0.27	-0.0206	0.0592	0.0496	-0.0924	0.0414	0.182	-0	0.5692	0.0837	-0.1277	0.7007	-0.0574	0.6071	256.8504	37.289	70.405
12	0.7555	-0.2218	0.0154	1.0727	-0.0109	0.4654	0.1279	-0.0129	-0.3127	-0.0811	0.0579	0.3876	0.1684	-0.0471	0	0.8304	0.0576	-0.1455	0.6014	0.0542	0.8639	227.7415	12.9183	71.7027

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 2 through 193 )	A	2 - 193
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 194 through 567 )	A	194 - 567
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 568 through 1212 )	A	568 - 1212
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1213 through 1406 )	A	0
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1407 through 1690 )	A	0
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1691 through 2167 )	A	0
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 193 )	B	2 - 193
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 194 through 567 )	B	194 - 567
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 568 through 1241 )	B	568 - 1241
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1242 through 1421 )	B	0
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1422 through 1812 )	B	0
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1813 through 2167 )	B	0

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