PDB-1ynj: Taq RNA polymerase-Sorangicin complex

ID or keywords:

Entry

Database: PDB / ID: 1ynj

Title

Taq RNA polymerase-Sorangicin complex

Components

(DNA-directed RNA polymerase ...) x 4

Keywords

TRANSFERASE

Function / homology

Function and homology information

DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function

PTS-regulatory domain, PRD - #20 / PTS-regulatory domain, PRD / DNA polymerase; domain 1 - #390 / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / : ...PTS-regulatory domain, PRD - #20 / PTS-regulatory domain, PRD / DNA polymerase; domain 1 - #390 / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / Enzyme I; Chain A, domain 2 / Topoisomerase I; Chain A, domain 4 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Gyrase A; domain 2 / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology

Biological species

Thermus aquaticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 3.2 Å

Authors

Campbell, E.A. / Pavlova, O. / Zenkin, N. / Leon, F. / Irschik, H. / Jansen, R. / Severinov, K. / Darst, S.A.

Citation

Journal: Embo J. / Year: 2005
Title: Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase
Authors: Campbell, E.A. / Pavlova, O. / Zenkin, N. / Leon, F. / Irschik, H. / Jansen, R. / Severinov, K. / Darst, S.A.

History

Deposition	Jan 24, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 15, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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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PDBx/mmCIF format	1ynj.cif.gz	644.8 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	1ynj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	1ynj_validation.pdf.gz	990.7 KB	Display	wwPDB validaton report
Full document	1ynj_full_validation.pdf.gz	1.1 MB	Display
Data in XML	1ynj_validation.xml.gz	119.9 KB	Display
Data in CIF	1ynj_validation.cif.gz	160.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yn/1ynj ftp://data.pdbj.org/pub/pdb/validation_reports/yn/1ynj	HTTPS FTP

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Related structure data

Related structure data	1ynnC C: citing same article (ref.)
Similar structure data	1ynn-d 5tmf-d 22446 3vkg-3 3dxj-2 7419 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	#253 - Jan 2021 Expressome similarity (9) #48 - Dec 2003 Catabolite Activator Protein similarity (11)

Deposited unit

A: DNA-directed RNA polymerase alpha chain

B: DNA-directed RNA polymerase alpha chain

C: DNA-directed RNA polymerase beta chain

D: DNA-directed RNA polymerase beta' chain

J: DNA-directed RNA polymerase beta' chain

K: DNA-directed RNA polymerase omega chain

hetero molecules

550 kDa, 6 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)	199.190, 199.190, 289.306
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

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DNA-directed RNA polymerase ... , 4 types, 6 molecules ABCDJK

#1: Protein	DNA-directed RNA polymerase alpha chain / RNAP alpha subunit / Transcriptase alpha chain / RNA polymerase alpha subunit Mass: 34830.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU8, DNA-directed RNA polymerase
#2: Protein	DNA-directed RNA polymerase beta chain / RNAP beta subunit / Transcriptase beta chain / RNA polymerase beta subunit Mass: 124930.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU7, DNA-directed RNA polymerase
#3: Protein	DNA-directed RNA polymerase beta' chain / RNAP beta' subunit / Transcriptase beta' chain / RNA polymerase beta' subunit Mass: 171187.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU6, DNA-directed RNA polymerase
#4: Protein	DNA-directed RNA polymerase omega chain / RNAP omega subunit / Transcriptase omega chain / RNA polymerase omega subunit Mass: 11642.423 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9EVV4, DNA-directed RNA polymerase

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Non-polymers , 2 types, 3 molecules

#5: Chemical	ChemComp-SRN / SORANGICIN A Mass: 807.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄₇H₆₆O₁₁
#6: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.82 Å³/Da / Density % sol: 65 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris, ammonium formate, magnesium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 20, 2004
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 3.2→40 Å / Num. all: 94908 / Num. obs: 93484 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 3.2→3.31 Å / % possible all: 98.5

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
CNS		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 3.2→40 Å / Cor.coef. F_o:F_c: 0.843 / Cor.coef. F_o:F_c free: 0.778 / SU B: 30.294 / SU ML: 0.515 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.618 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.34614	4504	5 %	RANDOM
R_work	0.28119	-	-	-
obs	0.28442	84957	93.09 %	-
all	-	91263	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 53.761 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.61 Å²	0 Å²	0 Å²
2-	-	0.61 Å²	0 Å²
3-	-	-	-1.21 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24309	0	60	0	24369

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.021	24825
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.475	1.979	33654
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.217	5	3145
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	3827
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	18877
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.262	0.2	13272
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.201	0.2	1002
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.232	0.2	85
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.087	0.2	4
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.733	1.5	15688
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.359	2	25197
X-RAY DIFFRACTION	r_scbond_it	1.256	3	9137
X-RAY DIFFRACTION	r_scangle_it	2.303	4.5	8457
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.2→3.283 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.412	316
R_work	0.368	6086

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	0.2028	0.0432	-0.2809	0.2995	-0.0528	0.9086	0.0483	-0.0297	-0.0384	0.1919	-0.0549	0.1036	-0.1952	-0.0056	0.0066	0.2967	-0.1758	0.0628	0.135	-0.1086	0.1782	39.467	84.457	52.708
2	-0.4921	0.9694	-2.4075	1.5815	-0.5776	4.1007	-0.0005	0.4705	-0.1483	0.0501	0.1062	-0.1488	-0.3616	-0.4974	-0.1057	0.3102	0	0	0.3101	0	0.3102	51.454	104.26	-3.577
3	-0.7591	3.0439	-1.581	4.2333	0.4651	0.9613	0.0434	0.2466	0.2191	0.3063	-0.1057	-0.2612	0.2744	-0.2514	0.0624	0.3102	0	0	0.3102	0	0.3102	67.531	127.908	16.347
4	0.5232	-2.3237	-0.9834	0.3631	2.777	-0.4406	0.2614	-0.0657	-0.102	0.2638	-0.2994	0.1116	0.3238	0.2055	0.038	0.3101	-0.0001	0.0002	0.3102	-0.0001	0.3101	50.111	62.777	9.768
5	1.8758	1.1582	-1.2281	-0.9726	0.4876	1.2483	0.0242	-0.1475	-0.0531	-0.0522	0.013	-0.1529	-0.1969	0.0796	-0.0372	0.3102	0	0	0.3102	0	0.3102	90.847	76.643	25.065
6	62.6625	-15.622	-12.2323	48.1566	-37.1515	85.5005	-0.7032	0.0397	-0.4268	-0.6154	0.405	1.1399	-2.6303	-2.7099	0.2982	0.3104	-0.0008	0.0004	0.3103	0.0001	0.3104	119.867	105.059	-9.493
7	70.9583	12.6586	-9.8904	42.5963	-16.9507	54.3931	0.1687	2.5514	-1.2824	-0.2923	-0.0389	1.654	1.3103	-0.6131	-0.1299	0.3101	0	0.0008	0.3101	0.0008	0.3104	131.2	96.491	-26.325
8	14.3805	3.0297	9.8227	6.9095	-0.3776	22.2344	-0.5307	-0.0966	0.2514	0.1865	0.5807	0.3071	-0.8217	0.3673	-0.05	0.3101	-0.0001	0.0001	0.3101	0.0001	0.3103	151.102	113.59	-43.414
9	16.8948	5.5259	-7.411	9.3306	1.7628	37.4922	0.73	-0.6042	0.9407	0.9881	-0.7442	-1.2412	-1.5018	0.1888	0.0143	0.3102	0.0002	0.0002	0.3105	-0.0001	0.31	132.529	92.93	1.218

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	6 - 235	6 - 235
2	X-RAY DIFFRACTION	1	B	B	4 - 228	4 - 228
3	X-RAY DIFFRACTION	1	C	C	1 - 21	1 - 21
4	X-RAY DIFFRACTION	1	C	C	131 - 141	131 - 141
5	X-RAY DIFFRACTION	1	C	C	325 - 335	325 - 335
6	X-RAY DIFFRACTION	1	C	C	393 - 704	393 - 704
7	X-RAY DIFFRACTION	1	C	C	829 - 1057	829 - 1057
8	X-RAY DIFFRACTION	1	D	D	620 - 1240	620 - 1240
9	X-RAY DIFFRACTION	1	J	E	1253 - 1435	1253 - 1435
10	X-RAY DIFFRACTION	1	J	E	1460 - 1501	1460 - 1501
11	X-RAY DIFFRACTION	1	K	F	1 - 95	1 - 95
12	X-RAY DIFFRACTION	1	D	H	1525	1
13	X-RAY DIFFRACTION	1	C	G	1120	1
14	X-RAY DIFFRACTION	2	C	C	22 - 130	22 - 130
15	X-RAY DIFFRACTION	2	C	C	336 - 392	336 - 392
16	X-RAY DIFFRACTION	3	C	C	142 - 324	142 - 324
17	X-RAY DIFFRACTION	4	C	C	705 - 828	705 - 828
18	X-RAY DIFFRACTION	5	C	C	1058 - 1114	1058 - 1114
19	X-RAY DIFFRACTION	5	D	D	3 - 162	3 - 162
20	X-RAY DIFFRACTION	5	D	D	451 - 619	451 - 619
21	X-RAY DIFFRACTION	5	J	E	1436 - 1459	1436 - 1459
22	X-RAY DIFFRACTION	5	D	I	1526	1
23	X-RAY DIFFRACTION	6	D	D	163 - 208	163 - 208
24	X-RAY DIFFRACTION	6	D	D	389 - 397	389 - 397
25	X-RAY DIFFRACTION	7	D	D	209 - 216	209 - 216
26	X-RAY DIFFRACTION	7	D	D	340 - 388	340 - 388
27	X-RAY DIFFRACTION	8	D	D	217 - 339	217 - 339
28	X-RAY DIFFRACTION	9	D	D	398 - 450	398 - 450

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