PDB-6drt: Crystal structure of the processivity clamp GP45 complexed with r...

ID or keywords:

Entry

Database: PDB / ID: 6drt

Title

Crystal structure of the processivity clamp GP45 complexed with recognition peptide of ligase from bacteriophage T4

Components

DNA polymerase clamp
GP45 recognition loop

Keywords

GENE REGULATION /

HYDROLASE / processivity clamp

Function / homology

Function and homology information

DNA ligase activity /

DNA ligase (ATP) /

DNA ligase (ATP) activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA polymerase processivity factor activity / viral transcription / DNA recombination /

DNA replication /

DNA repair ...
Similarity search - Function

Biological species

Enterobacteria phage T4 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.117 Å

Authors

Shi, K. / Aihara, H.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM095558	United States
National Science Foundation (NSF, United States)	MCB-0213124	United States

Citation

Journal: Nucleic Acids Res. / Year: 2018
Title: T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction.
Authors: Shi, K. / Bohl, T.E. / Park, J. / Zasada, A. / Malik, S. / Banerjee, S. / Tran, V. / Li, N. / Yin, Z. / Kurniawan, F. / Orellana, K. / Aihara, H.

History

Deposition	Jun 13, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 26, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 14, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6drt.cif.gz	296.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6drt.ent.gz	240.6 KB	Display	PDB format
PDBx/mmJSON format	6drt.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/dr/6drt ftp://data.pdbj.org/pub/pdb/validation_reports/dr/6drt	HTTPS FTP

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Related structure data

Related structure data	5wfyC 6dt1C 1czdS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1czd-d 1b8h-d 1b77-d 6fvo-2 1lj7-1 5g4q-2 5g4q-1 3rb9-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	#150 - Jun 2012 Sliding Clamps similarity (5) #55 - Jul 2004 DNA Ligase similarity (6)

Deposited unit

A: DNA polymerase clamp

B: DNA polymerase clamp

C: DNA polymerase clamp

D: GP45 recognition loop

E: GP45 recognition loop

F: GP45 recognition loop

hetero molecules

82.8 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	63.757, 90.950, 151.403
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	DNA polymerase clamp / DNA polymerase accessory protein 45 / DNA polymerase sliding clamp / Gp45 Mass: 25952.377 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 45 / Production host: Escherichia coli (E. coli) / References: UniProt: P04525
#2: Protein/peptide	GP45 recognition loop / GP45 recognition loop Mass: 1510.686 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T4 (virus) / References: UniProt: P00970
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.81 Å³/Da / Density % sol: 56.16 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.117→63.76 Å / Num. obs: 50401 / % possible obs: 99.1 % / Redundancy: 2.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.061 / R_sym value: 0.061 / Net I/σ(I): 15.7
Reflection shell	Resolution: 2.117→2.23 Å / Redundancy: 5.1 % / R_merge(I) obs: 1.34 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4893 / CC_1/2: 0.562 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
PHENIX	1.14rc1_3161	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1czd

1czd

Resolution: 2.117→33.783 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2403	2549	5.07 %
R_work	0.1988	-	-
obs	0.2009	50246	98.66 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.117→33.783 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5514	0	28	306	5848

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.001	5626
X-RAY DIFFRACTION	f_angle_d	0.368	7607
X-RAY DIFFRACTION	f_dihedral_angle_d	9.006	3372
X-RAY DIFFRACTION	f_chiral_restr	0.044	884
X-RAY DIFFRACTION	f_plane_restr	0.003	983

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 (%)
2.1173-2.158	0.3518	139	0.3088	2528	X-RAY DIFFRACTION	96
2.158-2.202	0.3151	137	0.2989	2657	X-RAY DIFFRACTION	100
2.202-2.2499	0.3472	137	0.3301	2569	X-RAY DIFFRACTION	98
2.2499-2.3022	0.3682	145	0.3082	2593	X-RAY DIFFRACTION	98
2.3022-2.3598	0.3192	133	0.2706	2667	X-RAY DIFFRACTION	100
2.3598-2.4235	0.3129	138	0.2552	2624	X-RAY DIFFRACTION	100
2.4235-2.4948	0.3093	153	0.2564	2641	X-RAY DIFFRACTION	100
2.4948-2.5753	0.2902	157	0.2482	2646	X-RAY DIFFRACTION	100
2.5753-2.6673	0.2947	153	0.2303	2647	X-RAY DIFFRACTION	99
2.6673-2.7741	0.2941	144	0.2337	2650	X-RAY DIFFRACTION	99
2.7741-2.9003	0.2598	148	0.23	2643	X-RAY DIFFRACTION	99
2.9003-3.0531	0.2589	147	0.2217	2629	X-RAY DIFFRACTION	99
3.0531-3.2442	0.2443	119	0.2181	2694	X-RAY DIFFRACTION	99
3.2442-3.4945	0.283	135	0.1994	2665	X-RAY DIFFRACTION	99
3.4945-3.8457	0.2127	142	0.1923	2656	X-RAY DIFFRACTION	98
3.8457-4.4012	0.2151	132	0.1624	2675	X-RAY DIFFRACTION	98
4.4012-5.5411	0.1785	140	0.1513	2700	X-RAY DIFFRACTION	98
5.5411-33.7876	0.1891	150	0.1628	2813	X-RAY DIFFRACTION	97

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	1.7905	1.4221	-0.741	7.1184	-2.1486	1.7972	0.1158	-0.1819	0.0326	0.4096	-0.08	0.2243	0.0916	-0.1065	-0.0281	0.4313	-0.0033	0.0091	0.3355	-0.0469	0.2969	-5.5762	-13.7421	29.1519
2	0.8416	-2.5873	-0.4388	8.8549	0.8465	1.6691	-0.289	-0.1683	0.2437	1.795	0.1581	-0.777	-0.2712	0.2025	0.161	0.624	-0.0096	-0.1119	0.4696	-0.0881	0.5044	2.0113	5.0851	33.2774
3	2.4821	2.4004	0.9505	2.4504	1.202	7.2062	-0.0665	0.2843	0.1577	-0.1883	-0.1384	0.2515	0.2942	-0.3605	0.1946	0.5372	0.1135	-0.0796	0.447	-0.0382	0.4608	-7.3944	8.8949	11.5355
4	8.116	-0.9837	-2.808	2.3989	1.0547	6.2971	0.5864	0.3306	0.4803	-0.6717	-0.3903	-0.3222	-0.6592	0.0463	-0.1797	0.5493	0.0852	0.0556	0.3421	-0.0108	0.5808	4.1109	15.553	8.7067
5	2.7606	-0.6619	-0.0442	4.2441	-2.232	4.0103	0.1339	-0.1445	0.4914	0.0849	-0.1476	0.0339	-0.2818	0.0599	-0.0037	0.4507	0.0369	-0.013	0.3337	-0.0848	0.5105	-2.163	12.8726	21.0732
6	0.0483	-0.0013	0.0315	0.241	-0.164	0.1482	0.0107	0.0769	0.932	0.5427	-0.0668	-0.3443	-1.0806	-0.1519	0.4022	0.9509	-0.0207	-0.0639	0.6413	0.154	1.1555	8.0374	21.5301	22.2753
7	1.3743	0.2771	-0.047	2.3465	1.2547	3.0909	-0.1021	0.037	0.2702	-0.009	0.077	0.0988	-0.5315	-0.3577	0.054	0.467	0.1166	-0.0308	0.4242	0.0548	0.441	-5.0882	8.4639	-14.2347
8	3.7094	0.1037	0.4544	6.4446	-0.6015	3.0351	-0.0772	0.4003	-0.0385	-0.4591	0.0336	-0.0256	0.0802	-0.2755	0.0492	0.3164	-0.04	0.0176	0.612	-0.018	0.3402	-8.2828	-15.4042	-29.9731
9	1.3098	-0.1684	-0.0612	2.1972	-2.2584	5.4632	-0.1079	0.3161	-0.0778	-0.2483	0.0928	-0.0678	0.2693	0.0243	-0.0144	0.3959	-0.0839	-0.0176	0.4213	-0.0475	0.408	-13.3441	-38.7635	-9.7361
10	5.4457	3.5468	1.1186	6.9099	-0.7921	5.4179	0.036	-0.0152	0.4426	0.426	0.2417	0.5081	-0.8138	-0.0116	-0.2426	0.4216	0.0373	-0.0128	0.3374	-0.0382	0.456	-14.4567	-32.2778	16.9047
11	6.2192	-1.499	-0.1063	4.8138	0.8926	6.0802	-0.1421	-0.4116	-0.4231	0.2295	0.0746	0.0893	0.1532	0.3079	0.0856	0.3708	0.011	-0.0668	0.3763	0.0559	0.416	-6.9788	-39.4855	23.812
12	1.8315	0.8083	-0.7215	4.2005	-1.9087	4.8197	0.0321	-0.1387	-0.217	0.1386	0.1242	0.0045	0.3493	0.0282	-0.1028	0.417	-0.0006	-0.0152	0.3552	-0.0551	0.4154	-12.3066	-46.0183	14.0197
13	8.0399	-0.2273	-0.9349	3.0007	3.0266	3.1177	-0.0966	-1.5954	2.1419	0.6258	0.264	-0.324	0.0949	1.7607	-0.1041	0.7984	-0.0217	-0.2145	0.8407	-0.2081	0.8482	8.7699	6.0169	31.7322
14	4.6025	-4.2927	-5.8792	4.4214	4.5707	9.4598	0.0858	-0.4936	-0.6662	-0.4424	1.2375	-0.1294	0.7008	0.722	-1.2497	0.8558	0.1444	0.1215	0.8751	0.1117	1.1749	6.8193	-6.2553	-32.6488
15	3.1707	0.719	2.8666	6.104	3.3132	3.8125	-0.722	0.7049	0.539	-0.4755	-1.405	-2.1505	-0.2931	2.0859	2.1182	0.9885	-0.2831	0.1948	1.3183	0.1813	1.2755	2.2293	2.1939	-34.1931
16	5.7273	-2.3707	0.8258	2.0587	1.0993	2.0484	0.5388	1.0622	-1.3735	-0.9387	-0.1879	-1.5848	0.7508	0.5408	-0.4509	0.896	0.171	0.0342	0.6107	-0.0456	1.0857	-5.2089	-53.7643	4.5938

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1001 through 1099 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1100 through 1113 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1114 through 1133 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1134 through 1164 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1165 through 1219 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1220 through 1230 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1001 through 1113 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1114 through 1228 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1001 through 1113 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1114 through 1132 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1133 through 1186 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1187 through 1230 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 229 through 237 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 227 through 231 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 232 through 237 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 229 through 237 )

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