PDB-5x06: DNA replication regulation protein

ID or keywords:

Entry

Database: PDB / ID: 5x06

Title

DNA replication regulation protein

Components

DNA polymerase III subunit beta
DnaA regulatory inactivator Hda

Keywords

REPLICATION / DNA replication / RIDA

Function / homology

Function and homology information

DNA polymerase III complex / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function

Biological species

Escherichia coli O157:H7 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.237 Å

Authors

Kim, J. / Cho, Y.

Funding support

Korea, Republic Of, 3items

Organization	Grant number	Country
National Research Foundation of Korea funded by the Korea Government	NRF-2015R1A2A1A05001694	Korea, Republic Of
National Research Foundation of Korea funded by the Korea Government	2012054226	Korea, Republic Of
National Research Foundation of Korea funded by the Korea Government	20120008833	Korea, Republic Of

Citation

Journal: To Be Published
Title: Replication regulation protein
Authors: Kim, J. / Cho, Y.

History

Deposition	Jan 20, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 24, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5x06.cif.gz	935.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5x06.ent.gz	784.9 KB	Display	PDB format
PDBx/mmJSON format	5x06.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5x06_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	5x06_full_validation.pdf.gz	1.6 MB	Display
Data in XML	5x06_validation.xml.gz	81.1 KB	Display
Data in CIF	5x06_validation.cif.gz	105.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/5x06 ftp://data.pdbj.org/pub/pdb/validation_reports/x0/5x06	HTTPS FTP

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Related structure data

Related structure data	2polS 3bosS S: Starting model for refinement
Similar structure data	6ed3-d 6b46-d 5wer-d 5ur2-4 21359 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	#168 - Dec 2013 DNA Helicase similarity (3) #150 - Jun 2012 Sliding Clamps similarity (8)

Deposited unit

A: DNA polymerase III subunit beta

B: DNA polymerase III subunit beta

C: DNA polymerase III subunit beta

D: DNA polymerase III subunit beta

E: DnaA regulatory inactivator Hda

F: DnaA regulatory inactivator Hda

G: DnaA regulatory inactivator Hda

H: DnaA regulatory inactivator Hda

hetero molecules

289 kDa, 8 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)	102.112, 149.542, 200.780
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein	DNA polymerase III subunit beta Mass: 42801.863 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: dnaN, Z5192, ECs4636 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A990, DNA-directed DNA polymerase
#2: Protein	DnaA regulatory inactivator Hda Mass: 28835.045 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: hda, Z3759, ECs3358 / Production host: Escherichia coli (E. coli) / References: UniProt: P69933

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Non-polymers , 4 types, 42 molecules

#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.84 Å³/Da / Density % sol: 56.71 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris-Cl pH 7.0, 10.5% PEG 400, 0.2M Calcium chloride, 10mM Trimethylamine-HCl, 1mM ADP, 5mM Magnesium chloride

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Data collection

Diffraction	Mean temperature: 103.15 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9786 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 24, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 3.23→50 Å / Num. obs: 49691 / % possible obs: 98.7 % / Redundancy: 6.6 % / R_sym value: 0.104 / Net I/σ(I): 36.2
Reflection shell	Resolution: 3.23→3.29 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.2 / R_sym value: 0.734 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2POL/3BOS

2pol

3bos

Resolution: 3.237→40.593 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2653	2469	5.05 %
R_work	0.2257	-	-
obs	0.2277	48864	98.25 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.237→40.593 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18098	0	136	30	18264

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	18566
X-RAY DIFFRACTION	f_angle_d	0.565	25149
X-RAY DIFFRACTION	f_dihedral_angle_d	15.942	11313
X-RAY DIFFRACTION	f_chiral_restr	0.04	2846
X-RAY DIFFRACTION	f_plane_restr	0.004	3261

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 (%)
3.2367-3.2989	0.3951	144	0.3471	2402	X-RAY DIFFRACTION	93
3.2989-3.3662	0.3893	143	0.3258	2565	X-RAY DIFFRACTION	100
3.3662-3.4394	0.3414	139	0.3063	2499	X-RAY DIFFRACTION	98
3.4394-3.5193	0.3166	142	0.2976	2575	X-RAY DIFFRACTION	98
3.5193-3.6073	0.3183	154	0.2988	2540	X-RAY DIFFRACTION	99
3.6073-3.7048	0.3414	140	0.2831	2541	X-RAY DIFFRACTION	98
3.7048-3.8137	0.3391	121	0.2681	2567	X-RAY DIFFRACTION	98
3.8137-3.9367	0.2663	135	0.2493	2572	X-RAY DIFFRACTION	98
3.9367-4.0773	0.2819	139	0.2351	2543	X-RAY DIFFRACTION	99
4.0773-4.2404	0.2707	135	0.222	2571	X-RAY DIFFRACTION	99
4.2404-4.4331	0.272	137	0.2051	2605	X-RAY DIFFRACTION	99
4.4331-4.6665	0.2264	130	0.1832	2620	X-RAY DIFFRACTION	100
4.6665-4.9584	0.2235	128	0.1847	2606	X-RAY DIFFRACTION	100
4.9584-5.3405	0.2287	140	0.2096	2637	X-RAY DIFFRACTION	100
5.3405-5.8765	0.2895	147	0.2354	2629	X-RAY DIFFRACTION	100
5.8765-6.7235	0.3074	115	0.2413	2691	X-RAY DIFFRACTION	100
6.7235-8.4583	0.2326	139	0.2049	2682	X-RAY DIFFRACTION	99
8.4583-40.5959	0.2148	141	0.1924	2550	X-RAY DIFFRACTION	91

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	3.7001	-3.9197	-0.7955	4.2723	1.5303	4.6655	-0.1409	-0.0832	-0.0709	-0.0739	-0.2139	0.3093	0.1572	0.281	0.1636	0.5009	-0.289	-0.163	0.7112	-0.0734	0.7985	-58.8631	-55.9992	-34.2544
2	3.0074	-0.2808	-1.4255	3.1068	0.1106	7.4601	-0.4114	-0.0975	0.0492	0.3387	-0.0838	0.1249	-0.3145	0.699	0.4006	0.5465	-0.1115	-0.1302	0.6125	-0.0298	0.6801	-53.4756	-52.9214	-29.071
3	3.4941	2.2005	-1.3875	3.3707	-0.5051	3.1078	0.2139	0.2057	1.137	-0.3549	0.3308	0.0211	-0.6683	0.3487	-0.1806	1.0234	-0.4062	0.0257	1.0798	0.2434	1.0566	-44.7987	-43.2005	-52.9217
4	2.5264	1.173	2.6567	3.7843	-0.267	5.7036	0.4433	0.7648	-1.4715	-1.3401	0.8932	0.1313	1.1266	1.0539	-0.676	1.2903	-0.0106	0.1642	1.4043	-0.3837	0.9865	-56.9816	-91.0255	-18.2827
5	3.9307	-1.439	-3.567	9.4008	-1.3153	7.9549	-0.1629	0.164	-0.4412	-1.1301	-0.2084	0.212	0.861	0.8154	0.0759	0.7442	0.0858	0.0454	0.9679	-0.0092	0.5471	-60.7108	-81.1562	-17.6632
6	2.015	3.4549	-2.1027	6.9295	-2.2396	7.0828	-0.0026	-1.497	0.366	2.0242	0.4668	-0.886	0.0768	0.9236	0.198	0.898	0.1332	-0.0993	1.4414	-0.2602	0.9672	-58.8373	-76.0399	-2.2495
7	5.6221	1.6104	0.1621	6.9216	0.8146	5.2559	-0.2178	-0.4382	0.1017	0.5804	0.1469	0.6994	-0.558	0.7338	0.0503	0.8331	0.0642	-0.0208	0.9765	-0.0239	0.5581	-63.7975	-73.346	-9.3729
8	8.2288	0.4697	-0.0857	5.8326	2.6323	7.5704	-0.6259	0.04	0.1064	-0.1561	0.7095	2.4562	-0.7686	-1.642	0.2331	0.7925	0.2127	-0.2315	0.6614	-0.0485	1.1448	-73.2474	-68.25	-14.4165
9	1.5254	-1.2125	0.5586	2.8728	-2.3869	3.0939	-0.2764	0.4006	0.5212	-2.2722	-0.0695	1.5176	-1.1237	-0.7636	0.6602	1.173	0.0051	-0.2053	0.9717	-0.1336	0.7867	-67.4522	-75.1544	-25.9842
10	7.6754	-2.5327	-7.0266	9.6136	5.8097	8.9901	-0.5497	2.2938	1.3939	-3.4049	-0.4634	-1.6777	-2.3092	-0.261	0.2386	2.0697	-0.0802	0.429	2.0031	-0.5997	1.3815	-65.7228	-96.5981	-32.3794
11	7.3655	-6.0641	-0.9057	9.0867	-4.3845	2.0062	-0.1601	-0.4082	0.0116	-0.7062	1.9341	1.8167	0.0197	-2.3541	-0.378	1.7324	-0.737	-0.2144	1.2833	0.0998	1.1264	-71.7688	-99.1776	-26.4909
12	6.2887	4.9589	2.4574	5.0091	2.5457	1.2646	0.9372	-1.4372	-0.8005	0.3251	-0.8649	-0.9945	-0.613	-0.7833	0.1952	1.3606	-0.1295	0.3367	0.9522	-0.0763	0.9941	-69.4294	-51.8212	54.2733
13	3.5382	1.3533	0.5315	9.8764	-2.4559	7.4502	0.02	0.1274	-0.4227	-0.3017	-0.367	0.2125	-0.3274	0.4498	0.4307	0.9391	-0.0639	0.4523	0.584	0.0332	1.3539	-62.4052	-47.7694	39.926
14	5.5832	-1.0177	3.0014	0.8757	-1.2036	2.2356	-0.4571	0.5241	1.5097	0.5152	-1.807	1.3637	-1.5135	-1.4108	0.8545	2.4357	-0.1823	0.0124	1.7599	-0.9956	2.085	-59.955	-44.0441	66.7606
15	2.049	-0.9076	2.2005	5.4334	-2.2516	2.6787	0.1867	-2.1138	0.6196	3.3074	-1.4697	-1.7661	-0.5832	-1.0152	0.8673	2.2074	-0.5304	-0.2946	2.1012	-0.1478	1.3998	-53.9894	-46.0353	71.3292
16	3.2569	-1.6955	-1.9843	6.2692	4.6254	3.6041	-0.4016	0.9754	-3.016	-0.3225	-1.1471	-0.3559	0.1579	-0.9633	0.8556	1.9108	-0.2705	0.1326	1.3021	0.1356	1.2407	-57.8118	-56.5928	70.8196
17	4.3202	1.1428	0.0233	3.5801	4.3391	7.489	0.2603	0.3574	-0.0118	-0.167	0.2795	-0.6172	0.8602	0.6695	-0.405	0.9923	-0.0786	-0.1835	0.6055	0.0407	0.7811	-34.5814	-14.9439	-15.4724
18	8.0061	0.08	-0.6598	1.9361	-0.0201	1.9285	0.1134	1.6189	-0.4662	-0.4897	-0.0216	0.2821	-0.1165	-0.2005	-0.1045	0.6608	0.0025	-0.1161	0.9061	-0.0364	0.6922	-66.37	-24.1553	-35.1146
19	4.3617	-0.071	-1.5762	2.3951	2.7663	5.2579	0.4067	-0.0703	0.1084	0.499	-0.3753	0.2866	-0.3659	-0.9552	0.0555	0.9767	-0.1203	-0.1989	0.8465	0.2	0.8326	-91.5278	-11.0134	-9.7629
20	7.0332	-0.673	-0.9583	1.2147	0.3651	2.6136	0.0591	-0.7368	0.8509	0.1878	-0.0635	-0.2165	-0.124	0.0453	0.0823	0.6635	-0.0599	-0.0011	0.5364	0.023	0.7245	-59.7668	-1.0371	9.5163
21	7.6364	1.96	-1.2331	4.4116	-1.824	5.774	-1.0146	-0.3555	-0.4955	-0.6851	0.3102	-0.162	0.8764	0.6053	0.6792	0.7897	0.0375	0.1321	0.8205	0.1388	0.7238	-69.4836	-24.9525	27.7487
22	7.4736	0.0151	0.4721	2.4047	-0.305	6.6973	-0.1898	-1.7611	0.5586	0.6464	-0.8322	-0.177	-0.0787	0.5609	1.0196	0.5878	0.0498	0.0961	1.6208	0.0507	0.7972	-76.6201	-16.4912	41.256
23	1.848	-2.1503	-0.2139	2.5005	0.0172	0.9838	-0.0088	1.2781	1.2229	-1.1164	0.7171	0.5899	0.3998	-0.825	-0.0479	1.2613	0.1737	-0.0607	1.2627	-0.0377	1.8691	-83.173	1.1797	37.3449
24	5.2102	0.7917	-0.7254	4.3401	2.3889	5.6221	0.1622	0.3569	-0.1031	-0.4569	0.0566	0.2054	0.7926	-0.4023	-0.1824	0.8322	-0.0994	0.0176	0.623	0.157	0.7056	-90.2771	-94.4155	19.1771
25	4.3849	0.4199	0.527	2.4412	-0.7118	2.7358	0.0708	0.7136	-0.8085	-0.4277	-0.0598	-0.4029	1.1374	0.723	-0.0519	1.0514	0.3233	0.0059	0.8943	-0.2311	0.7728	-55.0806	-102.2739	6.1813
26	5.4894	-1.7985	-2.325	6.9145	1.9908	7.7152	0.336	-0.2047	-0.5794	0.4808	-0.0511	-0.2235	0.542	1.1705	-0.2911	0.6605	0.069	-0.1268	0.9554	0.1064	0.769	-36.7274	-88.5825	35.2404
27	5.6487	-1.7194	-1.0843	1.0533	0.0556	0.8532	-0.058	-0.6039	0.02	0.6263	-0.1815	-0.2496	-0.2278	0.4546	0.1069	0.9276	-0.1689	-0.1064	1.0015	0.1225	0.9793	-50.9173	-79.8772	50.0274
28	6.3387	0.5428	-0.3683	2.6803	-0.2749	3.1992	0.1367	-1.4342	-0.1001	0.3945	0.0009	-0.0233	0.0954	0.4869	-0.1443	0.6766	-0.2029	0.0629	0.8761	0.0213	0.7193	-58.6067	-77.2849	52.4239
29	7.0796	1.4021	-0.312	4.8366	0.8289	4.581	0.0951	-0.3127	0.2559	0.058	-0.055	0.2198	-0.0875	-0.257	-0.0346	0.5679	-0.0756	0.1953	0.459	0.0738	0.7596	-85.7317	-80.245	45.9186

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'F' and (resid 4 through 55 )
2	X-RAY DIFFRACTION	2	chain 'F' and (resid 56 through 196 )
3	X-RAY DIFFRACTION	3	chain 'F' and (resid 197 through 231 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 5 through 27 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 28 through 86 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 87 through 95 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 96 through 136 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 137 through 154 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 155 through 166 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 167 through 179 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 180 through 208 )
12	X-RAY DIFFRACTION	12	chain 'G' and (resid 5 through 27 )
13	X-RAY DIFFRACTION	13	chain 'G' and (resid 28 through 166 )
14	X-RAY DIFFRACTION	14	chain 'G' and (resid 167 through 179 )
15	X-RAY DIFFRACTION	15	chain 'G' and (resid 180 through 201 )
16	X-RAY DIFFRACTION	16	chain 'G' and (resid 202 through 227 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid -1 through 123 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 124 through 365 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid -1 through 123 )
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 124 through 365 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 5 through 154 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 155 through 181 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 182 through 231 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid -1 through 123 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 124 through 365 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid -1 through 109 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 110 through 145 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 146 through 245 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 246 through 365 )

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