PDB-4k74: The UmuC subunit of the E. coli DNA polymerase V shows a unique i...

ID or keywords:

Entry

Database: PDB / ID: 4k74

Title

The UmuC subunit of the E. coli DNA polymerase V shows a unique interaction with the beta-clamp processivity factor.

Components

DNA polymerase III subunit beta
UmuC peptide

Keywords

DNA BINDING PROTEIN/TRANSFERASE / DNA replication clamp processivity factor / DNA replication/repair / DNA BINDING PROTEIN-TRANSFERASE complex

Function / homology

Function and homology information

DNA polymerase III complex / SOS response / 3'-5' exonuclease activity / DNA replication / damaged DNA binding / DNA-directed DNA polymerase activity / DNA repair / DNA binding / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Patoli, A.A. / Winter, J.A. / Bunting, K.A.

Citation

Journal: Bmc Struct.Biol. / Year: 2013
Title: The UmuC subunit of the E. coli DNA polymerase V shows a unique interaction with the beta-clamp processivity factor.
Authors: Patoli, A.A. / Winter, J.A. / Bunting, K.A.

History

Deposition	Apr 16, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 17, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k7/4k74 ftp://data.pdbj.org/pub/pdb/validation_reports/k7/4k74	HTTPS FTP

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Related structure data

Related structure data	3d1gS S: Starting model for refinement
Similar structure data	4n97-d 4k3q-d 6amq-1 4k3s-d 2xur-d 4mjr-d 3q4j-1 4n9a-d 4k3k-d 4mjp-d 3q4k-d 3q4j-2 4tsz-1 4k3p-d 4mjq-d 4n98-d 4ovg-d 3wgw-1 4n96-d 6pth-1 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	#150 - Jun 2012 Sliding Clamps similarity (8) #255 - Mar 2021 Cisplatin and DNA similarity (8) #91 - Jul 2007 Thymine Dimers similarity (7)

Deposited unit

A: DNA polymerase III subunit beta

B: DNA polymerase III subunit beta

C: UmuC peptide

D: UmuC peptide

85.6 kDa, 4 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)	79.520, 66.170, 82.730
Angle α, β, γ (deg.)	90.00, 114.99, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	SER	SER	A	A	1 - 18	7 - 24
2	1	MET	MET	SER	SER	B	B	1 - 18	7 - 24
1	2	PRO	PRO	GLU	GLU	A	A	28 - 52	34 - 58
2	2	PRO	PRO	GLU	GLU	B	B	28 - 52	34 - 58
1	3	VAL	VAL	ARG	ARG	A	A	54 - 80	60 - 86
2	3	VAL	VAL	ARG	ARG	B	B	54 - 80	60 - 86
1	4	SER	SER	PRO	PRO	A	A	101 - 117	107 - 123
2	4	SER	SER	PRO	PRO	B	B	101 - 117	107 - 123
1	5	LEU	LEU	ALA	ALA	A	A	119 - 147	125 - 153
2	5	LEU	LEU	ALA	ALA	B	B	119 - 147	125 - 153
1	6	ILE	ILE	LYS	LYS	A	A	231 - 264	237 - 270
2	6	ILE	ILE	LYS	LYS	B	B	231 - 264	237 - 270
1	7	GLN	GLN	LEU	LEU	C	C	357 - 360	6 - 9
2	7	GLN	GLN	LEU	LEU	D	D	357 - 360	6 - 9
1	8	LEU	LEU	MET	MET	A	A	155 - 182	161 - 188
2	8	LEU	LEU	MET	MET	B	B	155 - 182	161 - 188
1	9	ALA	ALA	LEU	LEU	A	A	266 - 283	272 - 289
2	9	ALA	ALA	LEU	LEU	B	B	266 - 283	272 - 289
1	10	VAL	VAL	MET	MET	A	A	285 - 364	291 - 370
2	10	VAL	VAL	MET	MET	B	B	285 - 364	291 - 370

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein	DNA polymerase III subunit beta Mass: 41459.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaN / Plasmid: pACYC-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1R4N6, DNA-directed DNA polymerase
#2: Protein/peptide	UmuC peptide Mass: 1322.444 Da / Num. of mol.: 2 / Fragment: beta binding peptide, UNP residues 353-363 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: Q8FI25, UniProt: A0A0H2V735*PLUS
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE CONNECTOR RESIDUE REQUIRED TO ATTACH THE FLUOROPHORE USED IN CRYSTALLISATION

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46.65 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 200 mM calcium acetate, 200 mM MES pH 6.5, 14% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.5→72.07 Å / Num. all: 24817 / Num. obs: 46830 / Redundancy: 1.9 % / B_iso Wilson estimate: 47.84 Å² / R_merge(I) obs: 0.062 / R_sym value: 0.062 / Net I/σ(I): 7.7
Reflection shell	Resolution: 2.5→2.64 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.284 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3670 / R_sym value: 0.025 / % possible all: 93.6

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
BALBES		phasing
REFMAC	5.5.0110	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3D1G

3d1g

Resolution: 2.5→70 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.864 / SU B: 24.951 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2947	2470	10 %	RANDOM
R_work	0.23145	-	-	-
obs	0.23746	22294	91.06 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 34.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.22 Å²	0 Å²	0.57 Å²
2-	-	1.7 Å²	0 Å²
3-	-	-	1 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→70 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5681	0	0	45	5726

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	5775
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3928
X-RAY DIFFRACTION	r_angle_refined_deg	1.372	1.98	7816
X-RAY DIFFRACTION	r_angle_other_deg	0.879	3	9600
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.171	5	724
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.435	24.318	264
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.301	15	1019
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.692	15	45
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	902
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	6393
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1106
X-RAY DIFFRACTION	r_nbd_refined
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
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.437	1.5	3643
X-RAY DIFFRACTION	r_mcbond_other	0.102	1.5	1463
X-RAY DIFFRACTION	r_mcangle_it	0.854	2	5878
X-RAY DIFFRACTION	r_scbond_it	1.525	3	2132
X-RAY DIFFRACTION	r_scangle_it	2.665	4.5	1938
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	265	TIGHT POSITIONAL	0.03	0.05
1	A	265	TIGHT THERMAL	0.07	0.5
2	A	291	TIGHT POSITIONAL	0.04	0.05
2	A	291	TIGHT THERMAL	0.09	0.5
3	A	345	TIGHT POSITIONAL	0.03	0.05
3	A	345	TIGHT THERMAL	0.08	0.5
4	A	225	TIGHT POSITIONAL	0.04	0.05
4	A	225	TIGHT THERMAL	0.08	0.5
5	A	396	TIGHT POSITIONAL	0.05	0.05
5	A	396	TIGHT THERMAL	0.09	0.5
6	A	490	TIGHT POSITIONAL	0.03	0.05
6	A	490	TIGHT THERMAL	0.07	0.5
7	C	52	TIGHT POSITIONAL	0.04	0.05
7	C	52	TIGHT THERMAL	0.58	0.5
8	A	353	TIGHT POSITIONAL	0.04	0.05
8	A	353	TIGHT THERMAL	0.09	0.5
9	A	252	TIGHT POSITIONAL	0.03	0.05
9	A	252	TIGHT THERMAL	0.11	0.5
10	A	990	TIGHT POSITIONAL	0.04	0.05
10	A	990	TIGHT THERMAL	0.09	0.5

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.413	174	-
R_work	0.32	1682	-
obs	-	-	92.8 %

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	1.7316	-1.9024	-1.0405	5.6554	-0.8713	3.8003	-0.0812	0.0783	-0.1972	-0.3195	-0.0014	-0.218	0.2734	-0.2845	0.0826	0.0803	-0.0136	0.0229	0.1961	-0.0003	0.1574	-19.3238	-2.3633	41.1339
2	1.266	-0.322	0.2356	1.3196	-0.0191	2.0698	-0.1372	-0.0854	-0.2451	0.0154	0.13	0.0045	0.0982	-0.1428	0.0072	0.0349	0.0261	0.0338	0.0937	0.0288	0.0704	-23.1703	0.1709	41.2348
3	9.5657	-4.462	-0.7747	6.558	-2.0297	1.3707	-0.0967	-0.4106	-0.1572	0.6893	0.2199	0.3391	-0.3036	0.0762	-0.1232	0.1397	0.0265	0.0283	0.2595	0.0707	0.0404	-20.6683	-2.4002	53.293
4	1.3964	-0.4825	0.6297	0.6887	0.3868	2.4226	-0.1047	-0.1058	-0.0325	-0.0468	0.0327	-0.0172	-0.0624	-0.3733	0.072	0.0631	-0.0462	0.0167	0.1437	0.0168	0.0803	-23.9302	1.6814	31.9868
5	1.5213	0.6057	-1.2226	16.3511	1.7887	1.3136	-0.0378	-0.0426	0.0524	0.214	0.1353	-0.1846	0.0245	0.0523	-0.0974	0.1098	-0.0047	0.0285	0.0762	0.0196	0.1034	-9.931	7.6044	14.3689
6	2.2838	-0.0599	-0.2038	0.0323	0.176	0.9937	0.072	0.2321	-0.1983	0.0027	-0.0611	-0.0013	0.0578	-0.2845	-0.0109	0.0582	0.0397	0.0128	0.1426	0.0059	0.1378	-18.9558	3.229	8.5852
7	3.6444	1.9366	-0.3771	8.5614	-2.3092	3.6013	0.0107	-0.2253	-0.4211	0.0566	-0.0671	-0.6832	0.0823	0.0707	0.0564	0.0647	-0.0267	0.0187	0.1506	-0.0076	0.095	-18.8785	0.4161	21.7918
8	3.6422	0.4555	-0.2443	0.3765	0.6613	2.5619	-0.0319	0.1952	0.2182	-0.0216	0.0453	0.0859	-0.1071	-0.4026	-0.0134	0.024	0.036	-0.018	0.1963	0.0442	0.0848	-25.0776	5.2509	20.6088
9	4.6852	-0.1633	0.5242	0.6651	0.5976	1.5066	0.0329	0.1325	0.2379	-0.1715	0.0096	0.0907	-0.1096	-0.1496	-0.0425	0.1176	0.0126	0.018	0.0974	0.0284	0.1123	2.1555	3.8963	2.3364
10	2.9736	-1.0726	0.3324	0.69	0.3818	1.8932	-0.029	0.273	0.0633	-0.0351	-0.0461	0.0933	0.0063	-0.0394	0.0751	0.0922	-0.0023	-0.0009	0.0778	0.0366	0.0872	4.4339	1.3454	0.5873
11	5.4744	0.1198	-1.4711	1.6922	0.1112	4.1607	-0.0772	-0.1798	-0.2892	0.155	0.0212	0.1687	0.3218	0.116	0.056	0.0485	-0.0043	-0.006	0.0567	0.0472	0.0855	26.3412	-5.992	19.3567
12	6.6394	-6.6321	-6.2307	7.5881	5.2958	6.7659	-0.388	0.2671	-0.1954	0.433	0.2799	0.1571	0.2189	-0.8078	0.1081	0.4247	-0.0194	-0.0166	0.3641	0.0196	0.4241	21.2306	12.5548	26.168
13	1.1644	0.3606	1.1315	2.3313	0.6509	2.8017	0.0622	-0.0373	-0.0543	-0.0554	-0.0521	-0.01	-0.0548	0.0434	-0.0101	0.0314	-0.0106	0.0247	0.0497	0.0014	0.053	28.9066	0.2743	17.7197
14	5.56	4.1306	4.5835	5.6122	3.0147	3.8941	-0.1429	0.0697	-0.0269	-0.228	0.1267	-0.1915	-0.162	-0.0003	0.0161	0.0757	0.0356	-0.0011	0.0994	0.0082	0.0212	28.0209	5.9849	13.408
15	2.5468	-0.5866	-1.0371	1.3765	0.4086	1.6866	-0.015	-0.0458	0.0816	-0.0607	-0.1187	-0.0372	-0.0837	0.1882	0.1337	0.0825	0.006	-0.0288	0.0659	0.023	0.0305	25.5371	1.2813	48.0974
16	2.0261	-0.0016	-1.0744	1.1794	-0.5732	1.4664	-0.0237	0.0593	0.0387	-0.1237	-0.0744	-0.1884	0.1058	0.0887	0.0981	0.0658	-0.013	-0.0093	0.0364	0.0184	0.0851	24.5928	-1.7906	46.3247
17	1.6543	-0.014	-0.8935	0.2282	-0.3327	1.3015	-0.053	-0.3091	0.1384	0.066	0.0158	-0.0857	-0.1184	0.1713	0.0371	0.0963	0.0253	-0.019	0.0729	-0.0099	0.0892	17.1359	0.9978	53.4761
18	2.7151	-0.6237	1.114	3.364	-1.7125	2.3581	-0.1822	-0.4094	0.2743	0.0896	0.2469	-0.0659	-0.2754	-0.341	-0.0647	0.0866	0.0723	0.0213	0.2525	-0.0392	0.0602	-6.4688	2.4824	61.5576
19	3.9992	1.5834	-1.4886	2.8839	-1.1779	2.1424	-0.0623	-0.2661	-0.0464	-0.1539	0.0435	-0.0327	0.1199	-0.378	0.0189	0.0632	0.0112	-0.0166	0.1843	-0.0089	0.0069	4.5428	-2.2991	59.8933
20	0.2742	0.6842	0.2481	2.018	0.8978	2.6284	0.018	-0.0208	0.0468	0.2854	0.123	-0.0337	0.1091	-0.0599	-0.141	0.1776	0.1041	-0.11	0.2259	-0.0611	0.089	10.3502	-0.2948	63.3205
21	0.205	-2.2072	0.6913	23.8054	-7.4615	2.3393	0.0035	0.0078	-0.0096	-0.1641	-0.0149	-0.0163	0.0524	-0.0038	0.0115	0.1369	-0.0503	0.0246	0.4407	-0.0126	0.4383	-5.8628	15.868	2.1401
22	0.5885	2.8946	-0.2246	21.9834	1.7705	1.1565	0.1445	-0.1614	0.0387	1.1098	-0.0982	0.2176	-0.0284	0.3087	-0.0463	0.3	0.1239	0.0079	0.4047	-0.0429	0.1145	11.9376	13.3237	61.9643

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 29
2	X-RAY DIFFRACTION	2	A	30 - 82
3	X-RAY DIFFRACTION	3	A	83 - 102
4	X-RAY DIFFRACTION	4	A	103 - 137
5	X-RAY DIFFRACTION	5	A	138 - 152
6	X-RAY DIFFRACTION	6	A	153 - 192
7	X-RAY DIFFRACTION	7	A	193 - 217
8	X-RAY DIFFRACTION	8	A	218 - 241
9	X-RAY DIFFRACTION	9	A	242 - 284
10	X-RAY DIFFRACTION	10	A	285 - 364
11	X-RAY DIFFRACTION	11	B	1 - 19
12	X-RAY DIFFRACTION	12	B	20 - 28
13	X-RAY DIFFRACTION	13	B	29 - 102
14	X-RAY DIFFRACTION	14	B	103 - 118
15	X-RAY DIFFRACTION	15	B	119 - 169
16	X-RAY DIFFRACTION	16	B	170 - 216
17	X-RAY DIFFRACTION	17	B	217 - 275
18	X-RAY DIFFRACTION	18	B	276 - 311
19	X-RAY DIFFRACTION	19	B	312 - 339
20	X-RAY DIFFRACTION	20	B	340 - 364
21	X-RAY DIFFRACTION	21	C	357 - 361
22	X-RAY DIFFRACTION	22	D	356 - 361

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