PDB-4ff1: N4 mini-vRNAP transcription initiation complex, 1 min after soaki...

ID or keywords:

Entry

Database: PDB / ID: 4ff1

Title

N4 mini-vRNAP transcription initiation complex, 1 min after soaking GTP, ATP and Mn

Components

Bacteriophag N4 P2 promoter
Virion RNA polymerase

Keywords

TRANSFERASE/DNA /

RNA polymerase /

DNA / TRANSFERASE-DNA complex

Function / homology

Function and homology information

DNA-directed RNA polymerase complex /

virion component / DNA-directed 5'-3' RNA polymerase activity /

DNA-directed RNA polymerase / GTP binding /

ATP binding /

metal ion binding
Similarity search - Function

Biological species

Enterobacteria phage N4 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.47 Å

Authors

Murakami, K.S. / Basu, R.S.

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: Watching the Bacteriophage N4 RNA Polymerase Transcription by Time-dependent Soak-trigger-freeze X-ray Crystallography.
Authors: Basu, R.S. / Murakami, K.S.

History

Deposition	May 30, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 12, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2013	Group: Database references
Revision 1.2	Feb 20, 2013	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _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	4ff1.cif.gz	910.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4ff1.ent.gz	739.8 KB	Display	PDB format
PDBx/mmJSON format	4ff1.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/ff/4ff1 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/4ff1	HTTPS FTP

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Related structure data

Related structure data	4ff2C 4ff3C 4ff4C C: citing same article (ref.)
Similar structure data	3c2p-1 3c3l-1 4ff3-2 4ff4-2 4ff4-1 3c3l-2 2po4-d 3c46-2 3c2p-2 3c46-1 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	#255 - Mar 2021 Cisplatin and DNA similarity (2) #67 - Jul 2005 TATA-Binding Protein similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #253 - Jan 2021 Expressome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #40 - Apr 2003 RNA Polymerase similarity (2) #227 - Nov 2018 Telomerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #135 - Mar 2011 Integrase similarity (1) #23 - Nov 2001 DNA similarity (2) #87 - Mar 2007 Zinc Fingers similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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similarity (1)
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Deposited unit

A: Virion RNA polymerase

C: Bacteriophag N4 P2 promoter

B: Virion RNA polymerase

D: Bacteriophag N4 P2 promoter

hetero molecules

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

1

A: Virion RNA polymerase

C: Bacteriophag N4 P2 promoter

hetero molecules

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

2

B: Virion RNA polymerase

D: Bacteriophag N4 P2 promoter

hetero molecules

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

Unit cell

Length a, b, c (Å)	82.163, 111.500, 277.103
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Virion RNA polymerase Mass: 123193.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage N4 (virus) / Plasmid: PKMK56 / Production host: Escherichia coli (E. coli) / References: UniProt: Q859P9
#2: DNA chain	Bacteriophag N4 P2 promoter Mass: 11022.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Bacteriophage N4 P2 promoter DNA
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.36 Å³/Da / Density % sol: 47.98 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M TRIS-HCL, 0.21 M DIBASIC AMMONIUM CITRATE, 0.09 M AMMONIUM DIHYDROGEN MONOPHOSPHATE, 25 % (DROP) 15% (RESERVOIR) PEG 3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 7, 2010
Radiation	Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.918 Å / Relative weight: 1
Reflection	Resolution: 2.47→50 Å / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 %

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: dev_1042)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.47→47.84 Å / SU ML: 0.3 / σ(F): 1.39 / Phase error: 19.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2111	4416	4.98 %	RANDOM
R_work	0.1534	-	-	-
obs	0.1563	88717	95.18 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.47→47.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16908	826	10	656	18400

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	18104
X-RAY DIFFRACTION	f_angle_d	1.075	24662
X-RAY DIFFRACTION	f_dihedral_angle_d	16.42	6878
X-RAY DIFFRACTION	f_chiral_restr	0.072	2826
X-RAY DIFFRACTION	f_plane_restr	0.005	3086

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 (%)
2.4609-2.4889	0.2698	129	0.2057	2544	X-RAY DIFFRACTION	87
2.4889-2.5182	0.3112	142	0.2112	2726	X-RAY DIFFRACTION	94
2.5182-2.5489	0.3175	143	0.2077	2760	X-RAY DIFFRACTION	95
2.5489-2.5811	0.2748	149	0.2005	2764	X-RAY DIFFRACTION	94
2.5811-2.6151	0.276	144	0.1983	2788	X-RAY DIFFRACTION	96
2.6151-2.6509	0.2861	146	0.1935	2759	X-RAY DIFFRACTION	94
2.6509-2.6888	0.3119	146	0.1897	2764	X-RAY DIFFRACTION	96
2.6888-2.7289	0.2787	152	0.1832	2823	X-RAY DIFFRACTION	95
2.7289-2.7716	0.259	145	0.1834	2758	X-RAY DIFFRACTION	95
2.7716-2.817	0.2671	146	0.1773	2777	X-RAY DIFFRACTION	95
2.817-2.8656	0.2471	147	0.1759	2779	X-RAY DIFFRACTION	95
2.8656-2.9177	0.2644	150	0.1813	2781	X-RAY DIFFRACTION	95
2.9177-2.9738	0.2589	143	0.1795	2752	X-RAY DIFFRACTION	94
2.9738-3.0345	0.2563	145	0.1827	2775	X-RAY DIFFRACTION	95
3.0345-3.1004	0.2452	143	0.1778	2803	X-RAY DIFFRACTION	95
3.1004-3.1725	0.2332	143	0.1698	2765	X-RAY DIFFRACTION	95
3.1725-3.2519	0.2557	148	0.1793	2798	X-RAY DIFFRACTION	95
3.2519-3.3398	0.2045	147	0.1682	2773	X-RAY DIFFRACTION	95
3.3398-3.438	0.2156	147	0.1598	2810	X-RAY DIFFRACTION	95
3.438-3.549	0.2429	146	0.1609	2815	X-RAY DIFFRACTION	95
3.549-3.6758	0.2376	149	0.1529	2787	X-RAY DIFFRACTION	96
3.6758-3.8229	0.18	148	0.1414	2842	X-RAY DIFFRACTION	96
3.8229-3.9968	0.1804	151	0.1328	2846	X-RAY DIFFRACTION	96
3.9968-4.2074	0.1819	148	0.1222	2863	X-RAY DIFFRACTION	96
4.2074-4.4708	0.1464	145	0.1145	2894	X-RAY DIFFRACTION	97
4.4708-4.8157	0.1485	154	0.1121	2902	X-RAY DIFFRACTION	97
4.8157-5.2998	0.1723	150	0.1197	2919	X-RAY DIFFRACTION	98
5.2998-6.0653	0.1834	155	0.1389	2932	X-RAY DIFFRACTION	97
6.0653-7.6367	0.1787	157	0.136	2949	X-RAY DIFFRACTION	96
7.6367-47.8489	0.1447	158	0.1324	3053	X-RAY DIFFRACTION	95

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	0.6721	-0.1063	0.2864	1.2487	0.2905	1.2015	-0.0302	-0.0437	0.0519	-0.0204	-0.0196	0.048	-0.0097	-0.0895	0.027	0.16	0.0182	-0.0164	0.2004	0.0078	0.1597	21.132	-45.4271	400.4084
2	0.5931	0.0494	0.0466	0.5986	0.0876	0.6162	-0.0216	0.0602	-0.0428	-0.0545	0.0144	-0.0996	0.0274	0.0658	0.0093	0.1445	-0.0215	0.0008	0.1716	-0.0063	0.1651	14.5187	-38.9864	362.9466
3	1.1989	0.1417	0.2288	1.2241	-0.4827	0.7739	-0.0219	0.1739	-0.0929	-0.2269	0.016	-0.3115	0.083	-0.0506	0.0007	0.2842	-0.0861	0.045	0.2543	0.0174	0.4264	33.0855	-11.1849	363.147
4	0.3084	-0.3482	0.2258	0.7297	-0.2711	0.2808	-0.1511	-0.1059	0.029	0.1581	0.1158	-0.0559	-0.1912	-0.0434	0.0154	0.2486	-0.0077	-0.0053	0.2615	-0.0348	0.1991	14.1576	-19.1359	390.8343
5	0.4752	-0.2393	-0.2265	0.5496	-0.0941	1.5	0.0039	0.0169	0.0787	0.0189	0.0387	0.0772	-0.3363	-0.0934	-0.0132	0.1953	0.0075	-0.0041	0.1869	-0.0019	0.1988	-3.8917	-17.4756	372.7881
6	1.2415	0.1292	0.4904	0.118	0.3563	1.0744	0.095	-0.0269	0.2904	-0.0369	-0.0178	-0.0797	-0.1551	0.1663	-0.0006	0.6068	-0.1565	-0.0566	0.5493	0.0629	0.5972	15.9975	-23.8275	384.8095
7	0.5655	-0.5227	-0.5548	0.9166	0.3947	2.0374	0.0072	-0.1142	0.3392	0.1001	0.1412	-0.3708	-0.44	0.1796	-0.1448	0.3529	-0.0358	-0.0569	0.25	-0.0221	0.3235	31.1611	-24.398	409.5769
8	0.9987	0.0194	-0.4772	1.1363	-0.3994	1.2881	0.0311	-0.0162	0.0154	-0.1218	-0.0105	-0.1166	-0.0727	0.0352	-0.0099	0.1648	-0.0039	0.0235	0.1692	-0.0093	0.1765	48.2282	-59.3195	403.3554
9	0.4794	-0.0591	-0.0716	0.9207	-0.1395	0.616	-0.0004	0.0129	0.022	-0.0432	0.0233	0.1559	-0.0164	-0.0128	-0.0257	0.1605	-0.0462	0.0166	0.1662	0.0075	0.189	63.9417	-63.9265	368.4826
10	1.5272	-0.1569	-0.2507	1.246	0.4131	0.8644	-0.1279	0.0722	0.0953	-0.3653	-0.0526	0.4405	-0.1165	0.0281	0.1249	0.3462	-0.0694	-0.09	0.269	-0.0057	0.394	43.5233	-89.7634	362.0052
11	0.333	-0.2437	-0.2357	0.4258	0.1638	0.404	-0.0664	-0.0597	-0.0471	0.0316	0.043	0.0802	0.1062	0.0083	0.0073	0.1934	-0.0166	0.0042	0.1957	0.0249	0.2115	56.6114	-85.0814	392.8584
12	0.1957	0.071	-0.143	0.6114	-0.3881	1.3552	0.0079	-0.0389	-0.1143	-0.0882	-0.0581	-0.1703	0.1708	0.244	0.0797	0.1347	0.0157	0.0089	0.2119	-0.0136	0.2292	77.8669	-88.4954	380.7942
13	2.1805	-0.6624	-1.5088	0.2519	0.7344	2.9174	0.0492	-0.0197	-0.0898	0.0479	0.2755	0.1727	-0.003	0.0541	-0.1816	0.5955	0.0442	0.0299	0.7194	0.0117	0.7222	55.555	-80.1523	387.9101
14	0.5058	-0.3003	0.3114	0.8026	-0.2971	2.0024	0.0307	0.0033	-0.3256	-0.0189	0.0981	0.0511	0.4414	-0.2362	-0.1425	0.2845	-0.0715	-0.0347	0.2267	-0.0018	0.3315	34.5426	-79.8533	407.8175

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 6:297)
2	X-RAY DIFFRACTION	2	(chain A and resid 298:619)
3	X-RAY DIFFRACTION	3	(chain A and resid 620:762)
4	X-RAY DIFFRACTION	4	(chain A and resid 763:921)
5	X-RAY DIFFRACTION	5	(chain A and resid 922:1100)
6	X-RAY DIFFRACTION	6	(chain C and resid 3:9)
7	X-RAY DIFFRACTION	7	(chain C and resid 10:22)
8	X-RAY DIFFRACTION	8	(chain B and resid 6:298)
9	X-RAY DIFFRACTION	9	(chain B and resid 299:619)
10	X-RAY DIFFRACTION	10	(chain B and resid 620:761)
11	X-RAY DIFFRACTION	11	(chain B and resid 762:934)
12	X-RAY DIFFRACTION	12	(chain B and resid 935:1100)
13	X-RAY DIFFRACTION	13	(chain D and resid 3:9)
14	X-RAY DIFFRACTION	14	(chain D and resid 10:22)

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Yorodumi