PDB-4khn: Crystal structure of the ternary complex of the D714A mutant of R...

ID or keywords:

Entry

Database: PDB / ID: 4khn

Title

Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase

Components

DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3')
DNA (5'-D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
DNA polymerase

Keywords

HYDROLASE / TRANSFERASE/dna / PALM SUBDOMAIN / TRANSFERASE / TRANSFERASE-dna complex

Function / homology

Function and homology information

bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...
Similarity search - Function

Biological species

Enterobacteria phage RB69 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Guja, K.E. / Jacewicz, A. / Trzemecka, A. / Plochocka, D. / Yakubovskaya, E. / Bebenek, A. / Garcia-Diaz, M.

Citation

Journal: Plos One / Year: 2013
Title: A Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site.
Authors: Jacewicz, A. / Trzemecka, A. / Guja, K.E. / Plochocka, D. / Yakubovskaya, E. / Bebenek, A. / Garcia-Diaz, M.

History

Deposition	Apr 30, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2013	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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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Download

PDBx/mmCIF format	4khn.cif.gz	794.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4khn.ent.gz	648.1 KB	Display	PDB format
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Validation report

Summary document	4khn_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	4khn_full_validation.pdf.gz	1.7 MB	Display
Data in XML	4khn_validation.xml.gz	65.9 KB	Display
Data in CIF	4khn_validation.cif.gz	91.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kh/4khn ftp://data.pdbj.org/pub/pdb/validation_reports/kh/4khn	HTTPS FTP

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Related structure data

Related structure data	4i9lC 4i9qC 3ngiS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4fjj-d 3suo-d 4fjm-d 4du4-d 4dtu-d 3suq-d 4du1-d 4e3s-d 4i9q-2 4m3y-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: DNA polymerase

C: DNA (5'-D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')

D: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3')

E: DNA (5'-D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')

F: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3')

B: DNA polymerase

hetero molecules

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

1

A: DNA polymerase

C: DNA (5'-D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')

D: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3')

hetero molecules

defined by author&software
116 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: DNA (5'-D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')

F: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3')

B: DNA polymerase

hetero molecules

defined by author&software
115 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.258, 119.353, 148.031
Angle α, β, γ (deg.)	90.00, 91.64, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	DNA polymerase / Gp43 Mass: 104519.039 Da / Num. of mol.: 2 / Mutation: D222A, D327A, Y567A, D714A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38087, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain	DNA (5'-D(TPCPAPCPGPTPAPAPGPCPAPGPTPCPCPGPCPG)-3') Mass: 5501.567 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain	DNA (5'-D(GPCPGPGPAPCPTPGPCPTPTPAPC)-3') Mass: 3967.585 Da / Num. of mol.: 2 / Source method*: obtained synthetically

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Non-polymers , 6 types, 319 molecules

#4: Chemical	ChemComp-XG4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.88 Å³/Da / Density % sol: 57.24 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 12% PEG 8000, 0.1 M MES, 0.2 Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6

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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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2013
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: 2.55→39.3 Å / Num. obs: 84020 / % possible obs: 99.9 % / Redundancy: 4.9 % / R_merge(I) obs: 0.063 / Net I/σ(I): 16.8
Reflection shell	Resolution: 2.55→2.559 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.617 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
CBASS		data collection
PHASER		phasing
PHENIX	(phenix.refine: dev_1363)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3NGI

3ngi

Resolution: 2.55→35.334 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 22.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2109	4149	4.94 %	RANDOM
R_work	0.1682	-	-	-
obs	0.1704	83990	99.85 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.55→35.334 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13909	1256	169	304	15638

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	15863
X-RAY DIFFRACTION	f_angle_d	1.192	21797
X-RAY DIFFRACTION	f_dihedral_angle_d	17.24	5840
X-RAY DIFFRACTION	f_chiral_restr	0.081	2355
X-RAY DIFFRACTION	f_plane_restr	0.005	2566

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 (%)
2.55-2.579	0.3017	138	0.2615	2631	X-RAY DIFFRACTION	100
2.579-2.6093	0.3105	132	0.266	2672	X-RAY DIFFRACTION	100
2.6093-2.6411	0.3434	120	0.2574	2686	X-RAY DIFFRACTION	100
2.6411-2.6745	0.2896	133	0.2482	2621	X-RAY DIFFRACTION	100
2.6745-2.7097	0.2867	127	0.2391	2675	X-RAY DIFFRACTION	100
2.7097-2.7468	0.2746	149	0.2271	2676	X-RAY DIFFRACTION	100
2.7468-2.7861	0.2969	126	0.2183	2619	X-RAY DIFFRACTION	100
2.7861-2.8276	0.2686	131	0.2089	2654	X-RAY DIFFRACTION	100
2.8276-2.8718	0.2614	133	0.203	2709	X-RAY DIFFRACTION	100
2.8718-2.9188	0.2495	122	0.1958	2623	X-RAY DIFFRACTION	100
2.9188-2.9692	0.2468	166	0.2031	2658	X-RAY DIFFRACTION	100
2.9692-3.0231	0.2541	124	0.1964	2647	X-RAY DIFFRACTION	100
3.0231-3.0812	0.2027	152	0.2003	2663	X-RAY DIFFRACTION	100
3.0812-3.1441	0.2507	116	0.211	2640	X-RAY DIFFRACTION	100
3.1441-3.2124	0.273	145	0.2071	2685	X-RAY DIFFRACTION	100
3.2124-3.2871	0.2567	132	0.191	2651	X-RAY DIFFRACTION	100
3.2871-3.3692	0.2479	140	0.1801	2658	X-RAY DIFFRACTION	100
3.3692-3.4602	0.2332	128	0.1798	2632	X-RAY DIFFRACTION	100
3.4602-3.562	0.2368	154	0.1697	2682	X-RAY DIFFRACTION	100
3.562-3.6768	0.2228	135	0.166	2647	X-RAY DIFFRACTION	100
3.6768-3.8081	0.2249	150	0.1597	2666	X-RAY DIFFRACTION	100
3.8081-3.9604	0.1796	150	0.1507	2635	X-RAY DIFFRACTION	100
3.9604-4.1404	0.1622	124	0.1366	2695	X-RAY DIFFRACTION	100
4.1404-4.3583	0.1699	140	0.1375	2643	X-RAY DIFFRACTION	100
4.3583-4.6308	0.1764	137	0.1273	2690	X-RAY DIFFRACTION	100
4.6308-4.9874	0.1701	129	0.1325	2659	X-RAY DIFFRACTION	100
4.9874-5.4876	0.1898	164	0.1445	2630	X-RAY DIFFRACTION	100
5.4876-6.2779	0.2187	139	0.1668	2699	X-RAY DIFFRACTION	100
6.2779-7.8949	0.2086	166	0.1675	2659	X-RAY DIFFRACTION	100
7.8949-35.3376	0.1563	147	0.1478	2736	X-RAY DIFFRACTION	100

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	1.4416	-2.0023	-0.07	5.0651	-0.4647	0.2628	0.2059	0.3761	0.0056	-0.8934	-0.2316	0.1089	0.1109	-0.0048	0.0331	0.5104	0.0438	-0.0675	0.4345	0.0036	0.3059	-7.4858	0.7978	-26.8746
2	2.9408	-0.7232	0.2249	3.4216	-1.1047	1.851	0.1831	0.2445	0.2553	-0.4916	-0.1709	-0.5402	-0.1504	0.1814	-0.0221	0.4133	0.0317	0.0986	0.3959	-0.0312	0.341	15.321	-20.8817	-19.4233
3	1.4206	-0.1999	-0.7665	0.6675	0.1062	1.366	-0.0301	0.0582	-0.298	-0.171	-0.0273	0.205	0.2277	-0.0828	0.0545	0.2763	-0.035	-0.0696	0.3232	-0.0336	0.3523	-11.397	-15.7684	-3.1875
4	0.9354	-0.6063	0.4428	1.0368	-0.3983	1.2058	0.0529	-0.0461	-0.1227	0.005	-0.0185	0.0342	0.0657	0.0995	-0.0375	0.2097	-0.0388	-0.0109	0.2876	-0.0613	0.2951	-4.9376	-17.3151	16.6243
5	7.9661	-0.4324	3.6893	4.1959	-2.1692	2.8997	-0.1328	0.0871	0.4724	0.4048	-0.112	-0.455	-0.327	0.7275	0.1698	0.2619	-0.0933	-0.0451	0.4284	-0.0618	0.4	4.4622	-1.2974	15.5019
6	9.136	2.8236	6.5822	5.6291	4.1278	9.1499	-0.1938	-1.3146	0.4616	0.6222	-0.1471	-0.2361	-0.6382	-0.3302	0.127	0.4637	-0.0237	-0.1114	0.5275	-0.0043	0.3759	4.1951	-3.2038	19.2864
7	4.5772	2.4115	3.3804	2.9946	3.1045	6.1043	0.0115	-0.1958	0.3201	-0.0438	0.0625	0.4894	-0.8973	-0.582	-0.1115	0.6871	0.1946	0.0355	0.4349	0.0127	0.4665	-41.5459	3.9409	-88.6318
8	6.8073	-5.6383	7.1427	5.7703	-5.7828	7.9772	-0.189	1.1743	0.1519	-0.3444	-0.2775	0.4225	-0.8678	0.3347	0.6512	1.0312	0.1252	-0.1902	0.7341	-0.0603	0.6244	-41.8126	2.417	-92.119
9	1.196	1.305	-0.2047	3.785	0.3879	-0.4029	0.3589	-0.3467	0.0878	1.2516	-0.2463	-0.0793	-0.3288	0.1245	-0.1023	1.7389	-0.2368	-0.0356	0.7986	-0.0335	0.4838	-32.9918	-3.8546	-50.4353
10	1.8363	0.1622	-0.8563	2.8753	0.5616	2.2712	0.2297	-0.4022	0.2172	0.9985	-0.3026	0.4362	-0.73	-0.0233	0.0499	1.3354	-0.1095	0.0811	0.5875	-0.0656	0.5213	-44.7933	-14.8384	-57.2206
11	2.4416	1.0502	0.2039	1.9827	0.1483	1.6405	0.3438	-0.2702	0.0404	0.7316	-0.2326	-0.426	-0.0616	-0.1204	-0.1076	0.8693	0.0228	-0.0671	0.4356	-0.1025	0.5564	-16.5019	5.4391	-75.5045
12	1.0359	-0.5386	-0.1976	5.4798	-2.1048	0.6308	0.0215	-0.1699	-0.4003	0.7449	-0.2683	-0.5142	0.2073	0.1811	0.1869	1.1822	0.0291	-0.1249	0.6282	-0.0093	0.6477	-16.3353	-16.9061	-70.7359
13	3.5405	3.0669	1.666	4.3671	1.2619	0.7038	0.0537	0.924	-0.8828	0.3251	0.497	-0.9033	0.2691	0.6482	-0.4811	0.6358	0.1788	-0.05	0.6385	-0.277	0.6929	-13.1925	-6.4643	-92.1233
14	7.8159	-1.1523	-1.2559	2.7299	1.1576	2.5935	0.0203	-0.1638	-0.135	0.3351	-0.0196	0.2457	0.3244	-0.0818	-0.0132	0.6796	0.0287	-0.0214	0.2993	0.0345	0.3488	-47.5571	-14.5259	-87.6698
15	3.6046	0.7072	-0.7286	0.9143	0.5179	2.5592	0.1182	0.285	-0.0121	0.1546	-0.0934	0.3546	0.1449	-0.169	-0.0891	0.4482	0.0802	-0.0218	0.3848	0.0272	0.4912	-46.3319	-17.8712	-101.4783

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 116 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 117 through 280 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 281 through 571 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 572 through 901 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 1 through 18 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 103 through 115 )
7	X-RAY DIFFRACTION	7	chain 'E' and (resid 1 through 18 )
8	X-RAY DIFFRACTION	8	chain 'F' and (resid 103 through 115 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 179 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 180 through 338 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 339 through 469 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 470 through 571 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 572 through 715 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 716 through 855 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 856 through 901 )

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