PDB-1pv4: X-ray crystal structure of the Rho transcription termination fact...

ID or keywords:

Entry

Database: PDB / ID: 1pv4

Title

X-ray crystal structure of the Rho transcription termination factor in complex with single stranded DNA

Components

5'-D(P*CP*C)-3'
Transcription termination factor rho

Keywords

Transcription/DNA / PROTEIN-ssDNA COMPLEX / Transcription-DNA COMPLEX

Function / homology

Function and homology information

ATP-dependent activity, acting on RNA / helicase activity / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIR,

MAD / Resolution: 3 Å

Authors

Skordalakes, E. / Berger, J.M.

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading
Authors: Skordalakes, E. / Berger, J.M.

History

Deposition	Jun 26, 2003	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 22, 2003	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Jan 31, 2018	Group: Experimental preparation / Category: exptl_crystal_grow Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4	Oct 9, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1pv4.cif.gz	473.8 KB	Display	PDBx/mmCIF format
PDB format	pdb1pv4.ent.gz	392.4 KB	Display	PDB format
PDBx/mmJSON format	1pv4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1pv4_validation.pdf.gz	521.1 KB	Display	wwPDB validaton report
Full document	1pv4_full_validation.pdf.gz	683 KB	Display
Data in XML	1pv4_validation.xml.gz	112.4 KB	Display
Data in CIF	1pv4_validation.cif.gz	144.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pv/1pv4 ftp://data.pdbj.org/pub/pdb/validation_reports/pv/1pv4	HTTPS FTP

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Related structure data

Related structure data	1pvoC C: citing same article (ref.)
Similar structure data	1pvo-d 1xpr-d 1xpu-d 1xpo-d 9386 6wa8-d 6059 6f0x-d 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	#219 - Mar 2018 Vacuolar ATPase similarity (2) #131 - Nov 2010 Inteins similarity (2) #72 - Dec 2005 ATP Synthase similarity (2)

Deposited unit

G: 5'-D(P*CP*C)-3'

H: 5'-D(P*CP*C)-3'

J: 5'-D(P*CP*C)-3'

K: 5'-D(P*CP*C)-3'

L: 5'-D(P*CP*C)-3'

A: Transcription termination factor rho

B: Transcription termination factor rho

C: Transcription termination factor rho

D: Transcription termination factor rho

E: Transcription termination factor rho

F: Transcription termination factor rho

290 kDa, 11 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	118.556, 204.327, 147.370
Angle α, β, γ (deg.)	90.00, 95.86, 90.00
Int Tables number	5
Space group name H-M	C121

#1: DNA chain	5'-D(PCPC)-3' Mass: 533.406 Da / Num. of mol.: 5 / Source method: obtained synthetically Details: Rho transcription termination factor is an essential gene in bacteria
#2: Protein	Transcription termination factor rho Mass: 47820.480 Da / Num. of mol.: 6 / Fragment: bacterial transcription termination Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RHO / Plasmid: PET24b / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG30
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.06 Å³/Da / Density % sol: 59.84 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M Nacacodylate (pH 6.5), 0.05M NaCl, 2.5% PEG 8K, 20% glycerol, 0.3mM n-Nonyl-beta-D-thiomaltoside, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 18K

Components of the solutions

ID	Name	Crystal-ID	Sol-ID
1	Nacacodylate	1	1
2	NaCl	1	1
3	PEG	1	1
4	glycerol,	1	1
5	n-Nonyl-beta-D-thiomaltoside	1	1
6	TCEP	1	1
7	H2O	1	1
8	PEG	1	2
9	NaCl	1	2
10	Nacacodylate	1	2
11	H2O	1	2

Crystal grow

*PLUS

Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details	Chemical formula
1	10 mM	Tris-HCl	1	drop	pH7.5
2	50 mM		1	drop		NaCl
3	100 mM	sodium cacodylate	1	reservoir	pH6.5
4	100 mM		1	reservoir		NaCl
5	5 %	PEG8000	1	reservoir
6	40 %	glycerol	1	reservoir
7	0.6 mM	n-Nonyl-beta-D-thiomaltoside	1	reservoir
8	2 mM	TCEP	1	reservoir
9			1
10			1
11			1

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	95	1
2		1
1,2		1

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.3.1 / Wavelength: 1.05, 1.0, 0.9794

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2002 / Details: mirrors

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	MAD	M	x-ray	1
2	SAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.05	1
2	1	1
3	0.9794	1

Reflection

Resolution: 3→50 Å / Num. all: 74391 / Num. obs: 63958 / % possible obs: 96.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.2 % / B_iso Wilson estimate: 89.4 Å² / R_sym value: 0.046 / Net I/σ(I): 15.5

Reflection shell

Resolution: 3→3.12 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.5 / R_sym value: 0.272 / % possible all: 98.5

Reflection

*PLUS

% possible obs: 97.9 % / R_merge(I) obs: 0.046

Reflection shell

*PLUS

% possible obs: 97.8 % / R_merge(I) obs: 0.272

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
SOLVE		phasing
MLPHARE		phasing
SHARP		phasing

Refinement

Method to determine structure:

SIR,

MAD / Resolution: 3→20 Å / Cor.coef. F_o:F_c: 0.887 / Cor.coef. F_o:F_c free: 0.864 / SU B: 19.137 / SU ML: 0.365 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.499 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29633	3379	5 %	RANDOM
R_work	0.26997	-	-	-
all	0.27132	77075	-	-
obs	0.27132	63958	97.9 %	-

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: 62.668 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.14 Å²	0 Å²	-2.27 Å²
2-	-	2.01 Å²	0 Å²
3-	-	-	-1.33 Å²

Refinement step

Cycle: LAST / Resolution: 3→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18846	190	0	41	19077

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	19317
X-RAY DIFFRACTION	r_angle_refined_deg	1.467	1.989	26029
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.735	5	2373
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	2989
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	14170
X-RAY DIFFRACTION	r_nbd_refined	0.311	0.2	10432
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.21	0.2	931
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.343	0.2	69
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.27	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	0.796	1.5	11903
X-RAY DIFFRACTION	r_mcangle_it	1.533	2	19211
X-RAY DIFFRACTION	r_scbond_it	2.16	3	7414
X-RAY DIFFRACTION	r_scangle_it	3.767	4.5	6818

LS refinement shell

Resolution: 3→3.076 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.43	238
R_work	0.403	4566

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	18.0662	-0.2108	-5.4212	10.0935	5.7184	12.8348	-0.6527	0.5463	-0.2075	0.1907	1.1275	-0.8463	0.8436	0.4566	-0.4748	0.6438	-0.1164	-0.1864	0.6161	-0.0807	0.6524	-12.81	-57.3047	-10.1208
2	8.7451	0.2107	2.8455	17.3935	1.0284	8.7896	-0.6628	-0.2925	-0.2497	0.4245	1.4532	1.7178	0.1395	-0.2462	-0.7904	0.2145	0.197	0.1068	1.0754	0.3116	1.0281	-51.3238	13.9924	28.5037
3	5.788	4.2679	-2.0752	5.3304	0.856	5.3623	0.1185	0.5275	0.8203	0.1159	0.047	0.2146	-0.4161	-0.2937	-0.1654	0.8924	0.2009	-0.0341	0.5788	0.2274	0.9141	-15.3358	47.3241	21.0809
4	7.7505	0.8771	-1.189	12.3171	-1.6344	1.5826	0.424	0.1005	0.6011	-1.1975	-0.2344	-0.6027	0.1882	0.4881	-0.1896	0.7885	-0.0507	0.2367	0.8733	0.2033	0.7072	30.9812	33.9318	8.6093
5	3.149	1.7859	2.5972	21.1452	-0.1244	3.2271	-0.4577	0.3356	-0.6607	-1.0484	0.549	-1.6138	0.1365	0.013	-0.0914	0.7581	0.2236	0.1257	0.751	-0.2797	0.7424	45.8525	-13.0925	9.949
6	-0.5294	-0.3702	0.4366	2.6327	2.7702	8.1232	-0.1104	0.0962	0.1087	-0.1584	-0.1557	0.448	0.217	-0.1909	0.2661	0.6882	-0.1473	-0.0591	0.6275	0.1571	0.9149	-24.7786	-44.0567	6.8957
7	2.1719	1.5634	1.4518	5.6293	1.6307	4.221	-0.1537	-0.0402	0.0473	-0.673	0.1492	1.7678	-0.2334	-0.5174	0.0045	0.2342	-0.0865	-0.101	0.7842	0.0645	1.2772	-46.5876	-12.5541	26.2665
8	2.7504	-0.0133	1.301	1.7799	-0.2072	3.0985	-0.0165	0.1572	0.1475	-0.189	0.2462	0.4374	-0.2479	-0.399	-0.2297	0.6905	0.215	-0.0359	0.8631	0.0285	0.8234	-33.8393	28.6128	27.9923
9	2.8583	-0.9579	0.6864	1.1328	-1.0238	2.7679	-0.0261	0.5486	0.4129	-0.214	0.0161	-0.1461	-0.2691	-0.0502	0.01	0.8469	-0.042	-0.0057	0.6639	0.0805	0.8283	6.4085	41.1795	18.3377
10	1.9315	-0.1601	1.3332	2.8909	-0.5518	2.4297	0.2617	0.2893	0.1093	-0.7721	0.0113	-0.1842	0.2256	0.1132	-0.273	0.8109	0.0702	0.176	0.9004	0.0526	0.669	38.7066	13.113	11.9763
11	3.9094	0.5498	3.4835	2.1133	-0.0273	7.475	0.0961	0.1468	-0.426	-0.3654	0.1441	-0.1395	0.6874	-0.2518	-0.2403	0.8964	0.1726	-0.1204	0.4996	-0.1445	0.779	35.9836	-28.6823	23.4128
12	2.2986	-0.5593	-1.0099	3.1511	0.806	4.0536	-0.0962	-0.2283	0.164	0.229	0.3709	-0.3984	0.086	0.7775	-0.2747	0.668	0.0244	-0.0805	0.7685	-0.0415	0.91	-8.3059	-33.5525	25.2661
13	0.3746	0.1312	-0.1214	3.177	1.1964	2.4585	-0.0632	-0.0245	-0.1258	0.4773	0.1661	0.1558	0.3136	-0.0009	-0.1029	0.7263	0.0231	0.1008	0.7651	0.0569	0.8756	-25.85	-12.2911	42.2435
14	1.2165	0.4432	0.122	1.9367	0.9195	1.577	-0.047	-0.1525	-0.1244	0.2162	0.1102	0.1197	0.0247	-0.0467	-0.0631	0.7713	0.1342	0.0645	0.8917	0.0263	0.7394	-17.7677	18.4434	46.7535
15	2.3092	0.1561	0.4571	1.0082	0.1999	0.4955	-0.0552	-0.2504	0.1594	0.0505	0.1203	-0.0347	-0.0225	-0.0418	-0.065	0.8347	0.0664	0.0373	0.8029	-0.0614	0.8066	11.7716	30.0349	41.8876
16	1.912	-0.7157	0.6742	1.3097	-0.2248	1.1387	0.0069	-0.062	0.1472	0.1331	0.0908	-0.1161	0.0326	-0.0022	-0.0977	0.7471	-0.0081	0.0285	0.8187	-0.0649	0.8285	38.1252	11.961	38.5944
17	1.9528	-0.117	1.4176	1.4835	-0.278	3.9626	0.2289	-0.091	-0.136	0.0633	-0.0026	-0.0085	0.4421	-0.0867	-0.2263	0.8907	0.0096	-0.1409	0.6868	-0.0488	0.6962	40.1766	-18.8297	47.7072
18	40.1437	6.2645	22.4845	74.3353	-1.3396	3.009	1.135	-0.4545	0.6444	2.4459	-0.6772	0.8216	0.9258	0.8736	-0.4578	0.8702	0.0014	-0.0009	0.8717	-0.0004	0.8701	1.3532	-47.0329	47.8229
19	32.113	-16.2591	-15.1627	40.3033	19.6856	69.1366	-0.6797	-1.0678	2.4721	2.5857	-1.7832	-0.1949	-0.9297	-0.5955	2.4629	0.8706	-0.001	0.0006	0.871	0.0011	0.8707	-25.2921	-18.0743	69.4255
20	8.2484	-7.6557	-2.5522	-18.1703	2.4613	14.944	0.5634	-0.3072	1.3962	0.5415	-0.1574	1.2874	0.7355	1.3579	-0.4059	0.8853	0.1145	-0.0026	0.8883	0.0504	0.8711	-18.0903	26.1164	73.2344
21	12.803	7.4899	14.3373	41.0387	0.8971	40.2409	0.4525	1.4332	0.5386	1.7067	-2.1152	-2.574	-0.5307	2.8643	1.6627	0.8713	0.0002	-0.0012	0.8696	-0.0013	0.8698	21.1749	43.4021	64.6002
22	26.6179	9.1386	-12.7037	25.7925	-19.1049	27.128	-1.4648	-3.9344	-0.8631	0.3344	-0.7441	-3.3907	2.4614	1.8247	2.2089	0.8715	-0.0008	-0.0029	0.8703	-0.0017	0.8699	58.6805	20.1171	55.5301
23	8.8719	-14.5872	17.1359	-12.4516	0.9064	25.9681	0.2631	0.606	-1.2446	0.4859	-0.2647	-1.2157	1.3644	0.9264	0.0016	0.8704	-0.0011	-0.0004	0.871	0.0007	0.87	61.1709	-23.4211	63.4361

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	F	1 - 46	1 - 46
2	X-RAY DIFFRACTION	2	C	H	1 - 46	1 - 46
3	X-RAY DIFFRACTION	3	D	I	1 - 46	1 - 46
4	X-RAY DIFFRACTION	4	E	J	1 - 46	1 - 46
5	X-RAY DIFFRACTION	5	F	K	1 - 46	1 - 46
6	X-RAY DIFFRACTION	6	A	F	47 - 155	47 - 155
7	X-RAY DIFFRACTION	7	B	G	51 - 155	51 - 155
8	X-RAY DIFFRACTION	8	C	H	47 - 155	47 - 155
9	X-RAY DIFFRACTION	9	D	I	47 - 155	47 - 155
10	X-RAY DIFFRACTION	10	E	J	47 - 155	47 - 155
11	X-RAY DIFFRACTION	11	F	K	47 - 155	47 - 155
12	X-RAY DIFFRACTION	12	A	F	156 - 400	156 - 400
13	X-RAY DIFFRACTION	13	B	G	156 - 400	156 - 400
14	X-RAY DIFFRACTION	14	C	H	156 - 400	156 - 400
15	X-RAY DIFFRACTION	15	D	I	156 - 400	156 - 400
16	X-RAY DIFFRACTION	16	E	J	156 - 400	156 - 400
17	X-RAY DIFFRACTION	17	F	K	156 - 400	156 - 400
18	X-RAY DIFFRACTION	18	A	F	401 - 417	401 - 417
19	X-RAY DIFFRACTION	19	B	G	401 - 417	401 - 417
20	X-RAY DIFFRACTION	20	C	H	401 - 417	401 - 417
21	X-RAY DIFFRACTION	21	D	I	401 - 417	401 - 417
22	X-RAY DIFFRACTION	22	E	J	401 - 417	401 - 417
23	X-RAY DIFFRACTION	23	F	K	401 - 417	401 - 417

Refinement

*PLUS

Highest resolution: 3 Å / Lowest resolution: 20 Å / % reflection R_free: 5 % / R_factor R_free: 0.296 / R_factor R_work: 0.27

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.014
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.47

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