PDB-4qjv: The X-ray crystal structure of Rpo3/Rpo11 heterodimer of euryarch...

ID or keywords:

Entry

Database: PDB / ID: 4qjv

Title

The X-ray crystal structure of Rpo3/Rpo11 heterodimer of euryarchaeal RNA polymerase from Thermococcus kodakarensis

Components

DNA-directed RNA polymerase subunit DPolymerase
DNA-directed RNA polymerase subunit LPolymerase

Keywords

TRANSFERASE /

Transcription /

RNA polymerase

Function / homology

Function and homology information

DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity /

DNA-directed RNA polymerase /

protein dimerization activity / DNA-templated transcription /

DNA binding /

cytoplasm
Similarity search - Function

Biological species

Thermococcus kodakarensis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.601 Å

Authors

Hirata, A. / Murakami, K.S.

Citation

Journal: Nat Commun / Year: 2014
Title: The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration
Authors: Jun, S.H. / Hirata, A. / Kanai, T. / Santangelo, T.J. / Imanaka, T. / Murakami, K.S.

History

Deposition	Jun 5, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 8, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 10, 2014	Group: Database references
Revision 1.2	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4qjv.cif.gz	315.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4qjv.ent.gz	258.6 KB	Display	PDB format
PDBx/mmJSON format	4qjv.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/qj/4qjv ftp://data.pdbj.org/pub/pdb/validation_reports/qj/4qjv	HTTPS FTP

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Related structure data

Related structure data	4qiwC C: citing same article (ref.)
Similar structure data	2z7e-d 5n76-d 5z7g-d 1npp-1 1m1g-3 2uzp-d 1k9a-1 1k9a-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 - 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	#40 - Apr 2003 RNA Polymerase similarity (7) #255 - Mar 2021 Cisplatin and DNA similarity (6) #241 - Jan 2020 Twenty Years of Molecules similarity (6)

Deposited unit

A: DNA-directed RNA polymerase subunit D

B: DNA-directed RNA polymerase subunit L

C: DNA-directed RNA polymerase subunit D

D: DNA-directed RNA polymerase subunit L

hetero molecules

81 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DNA-directed RNA polymerase subunit D

B: DNA-directed RNA polymerase subunit L

hetero molecules

defined by author&software
40.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: DNA-directed RNA polymerase subunit D

D: DNA-directed RNA polymerase subunit L

defined by author&software
40.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.598, 88.169, 102.907
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	DNA-directed RNA polymerase subunit D / Polymerase Mass: 29429.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: rpoD, TK1503 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q5JJF4, DNA-directed RNA polymerase
#2: Protein	DNA-directed RNA polymerase subunit L / Polymerase Mass: 11013.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: rpoL, TK1167 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q5JE88, DNA-directed RNA polymerase
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1121 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.74 %
Crystal grow	Temperature: 277 K / Method: microbatch crystallization / pH: 10 Details: 0.1M CAPS (pH 10), 0.1M ammonium dihydrogen phosphate, 34%(w/v) PEG4000, Microbatch crystallization, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X25 / Wavelength: 0.9785, 0.9788, 0.9600

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2006

Radiation

Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9785	1
2	0.9788	1
3	0.96	1

Reflection

Resolution: 1.6→50 Å / Num. obs: 91780 / % possible obs: 99.1 %

Reflection shell

Resolution: 1.6→1.66 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 9016 / R_sym value: 0.611 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
SnB		phasing
PHENIX	(phenix.refine: dev_1626)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 1.601→44.084 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.77 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2108	1998	2.18 %	RANDOM
R_work	0.1792	-	-	-
obs	0.1799	91663	99.4 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.601→44.084 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5647	0	5	1121	6773

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5843
X-RAY DIFFRACTION	f_angle_d	1.095	7915
X-RAY DIFFRACTION	f_dihedral_angle_d	13.278	2232
X-RAY DIFFRACTION	f_chiral_restr	0.044	885
X-RAY DIFFRACTION	f_plane_restr	0.006	1026

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.601-1.6413	0.2944	137	0.2273	6123	97
1.6413-1.6856	0.2524	139	0.2193	6325	99
1.6856-1.7353	0.2375	141	0.2088	6356	100
1.7353-1.7913	0.2452	142	0.1985	6361	100
1.7913-1.8553	0.219	143	0.1959	6381	100
1.8553-1.9296	0.241	142	0.1909	6374	100
1.9296-2.0174	0.2346	144	0.1889	6424	100
2.0174-2.1237	0.2217	142	0.1801	6388	100
2.1237-2.2568	0.222	144	0.1807	6437	100
2.2568-2.431	0.233	142	0.1741	6432	100
2.431-2.6757	0.2132	145	0.1828	6448	100
2.6757-3.0627	0.2193	145	0.1819	6500	100
3.0627-3.8584	0.1857	146	0.162	6535	100
3.8584-44.1012	0.1785	146	0.1678	6581	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	2.1968	1.067	-0.0186	1.7464	-0.2009	1.0109	-0.1447	0.1194	-0.053	-0.0752	0.0313	-0.2216	-0.0389	0.1459	0.0746	0.1214	0.0074	-0.0017	0.1516	0.0019	0.1204	44.2252	37.6345	86.3789
2	2.6514	0.1306	0.5691	0.2763	0.0241	0.4034	-0.0678	0.0825	0.2779	-0.0699	-0.0791	0.0201	-0.0974	-0.0021	0.137	0.1633	0.0129	-0.0364	0.1233	-0.008	0.1191	33.2216	53.8301	80.6019
3	1.0827	-0.1786	-0.1018	0.7579	0.0029	0.6875	-0.1008	0.0026	-0.0059	-0.25	0.0171	0.2246	0.0824	-0.0497	-0.0851	0.1496	0.0043	-0.0835	0.1554	-0.0248	0.1735	15.5008	50.2041	74.4537
4	0.8191	-0.3365	0.6121	0.4415	-0.5095	1.2684	-0.0945	-0.0724	0.0402	0.0264	0.0404	-0.02	-0.1639	-0.0439	0.0308	0.1245	0.008	-0.0137	0.1043	-0.0044	0.093	40.2615	45.0224	94.8846
5	1.4225	-1.086	0.8738	1.2057	-0.4078	1.8194	0.0282	-0.222	-0.1821	0.106	0.0735	0.1401	0.134	-0.0538	-0.0613	0.1376	0.0129	0.0091	0.1305	0.0164	0.1485	45.7612	28.4151	107.4877
6	1.477	0.1754	0.2999	1.1924	-0.2311	1.5834	-0.0468	-0.1092	0.1168	0.1267	0.0124	-0.0573	-0.0942	0.064	0.0202	0.1388	0.0068	0.0024	0.1669	-0.0047	0.1251	46.834	38.3872	109.1115
7	0.7536	0.3724	-0.1411	0.62	-0.2495	0.378	-0.0136	0.0377	0.0155	-0.1061	0.0073	0.0127	-0.0083	0.0155	0.0211	0.1509	0.0126	-0.0044	0.1358	-0.0053	0.1186	44.1577	51.557	77.439
8	1.0508	-0.1906	0.3356	1.4933	-0.3103	1.2471	-0.0063	-0.1715	0.0644	0.1485	0.0129	-0.0423	-0.0128	0.0749	-0.0175	0.1468	-0.01	-0.0061	0.1489	0.0029	0.1086	51.1868	67.851	82.1322
9	5.398	-0.3647	-0.4547	1.2172	0.1595	0.9932	0.0516	-0.0596	0.0789	0.1292	-0.0419	-0.0643	-0.0888	0.1689	0.0332	0.1155	-0.0137	-0.0009	0.1273	0.0168	0.0989	48.4049	70.3106	82.8236
10	0.927	1.4931	-0.248	4.5076	-0.1904	0.6375	-0.1481	0.143	-0.215	-0.4015	0.123	-0.4387	0.1004	0.0903	0.0073	0.1723	0.0178	0.0171	0.2034	0.0003	0.1547	53.1326	50.0323	76.1475
11	0.3907	0.3374	0.3977	0.346	0.2227	0.7733	-0.1821	-0.0926	0.1924	0.0559	-0.1778	0.5756	-0.1848	-0.2389	-0.1804	0.1025	0.0358	-0.0071	0.1235	-0.0786	0.4012	7.2659	70.8598	90.3199
12	0.4699	-0.2592	0.1832	1.5608	-0.0442	0.0646	0.014	0.0335	0.0211	0.0133	0.0044	-0.005	0.0077	0.0003	-0.0023	0.0932	0.0112	0.0263	0.1228	0.0058	0.0793	26.4647	51.6599	97.192
13	0.755	-0.3546	-0.342	2.2278	0.505	0.7784	0.0826	-0.0072	0.0099	0.119	-0.0851	0.2374	-0.0701	-0.1158	-0.0097	0.1524	0.023	0.0223	0.1536	-0.0087	0.1331	19.362	47.8332	106.2657
14	0.8469	-0.7517	-0.0173	2.7362	0.3615	1.009	0.0436	-0.074	-0.1129	0.1771	-0.0627	0.0871	0.1249	-0.1596	-0.0444	0.0932	-0.0091	0.0218	0.1121	0.0054	0.0976	25.3861	37.0608	102.1512
15	0.4781	0.1286	0.1461	0.5263	0.1822	0.3975	-0.1603	0.2601	0.1295	-0.5373	-0.0061	0.47	-0.1024	0.1033	-0.3037	0.4045	-0.0164	-0.2481	0.2333	0.0067	0.3179	11.217	66.9877	78.6226
16	0.4124	0.0596	-0.4803	0.3639	0.1073	0.6986	-0.1384	0.4887	0.2259	-0.988	0.0252	0.4493	-0.2526	-0.2005	-1.1743	0.8129	0.102	-0.5986	0.2614	0.0889	0.62	6.4381	73.6566	69.6263
17	0.9799	0.9324	-0.1788	2.003	-0.3392	1.5462	0.183	-0.2759	0.1947	0.3019	-0.2299	0.1979	-0.1002	-0.0256	-0.0184	0.1339	0.0033	0.0613	0.1755	-0.0213	0.1864	20.0526	71.2309	101.4236
18	1.9594	0.6296	0.781	3.1629	0.8097	1.3458	0.0691	-0.2627	0.1024	0.209	0.0724	0.0706	0.0383	0.0658	-0.1182	0.1828	-0.0374	-0.0482	0.2416	0.037	0.2805	40.3808	80.2482	102.534
19	1.0937	0.094	-0.01	1.6574	-0.2311	0.9333	-0.0285	0.1579	0.23	-0.0349	-0.034	0.1259	-0.159	0.0392	0.0757	0.1741	-0.0165	-0.0005	0.2197	0.0375	0.2502	31.8191	82.4883	92.6806
20	1.1133	0.906	0.0197	4.0918	-0.7849	0.9324	0.0052	-0.1789	-0.2439	-0.1099	0.0635	-0.3177	0.1443	0.1859	0.0788	0.2043	-0.0392	-0.0274	0.2416	0.0635	0.3412	39.6945	76.6507	96.5747
21	2.7664	0.9146	0.4801	0.7378	0.0497	0.953	-0.0172	-0.3134	0.5161	0.3136	-0.0687	0.575	-0.1103	-0.0807	0.1449	0.2912	0.0584	0.1254	0.2158	-0.0251	0.447	20.4012	83.1681	100.2214

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 22 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 47 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 48 through 138 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 139 through 167 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 168 through 187 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 188 through 215 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 216 through 259 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 46 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 47 through 66 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 67 through 94 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1 through 22 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 23 through 64 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 65 through 118 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 119 through 138 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 139 through 177 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 178 through 219 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 220 through 258 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 1 through 21 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 22 through 44 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 45 through 61 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 62 through 94 )

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