PDB-4khs: Ternary complex of RB69 mutant L415F with a ribonucleotide at 0 p...

ID or keywords:

Entry

Database: PDB / ID: 4khs

Title

Ternary complex of RB69 mutant L415F with a ribonucleotide at 0 position

Components

DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3')
DNA polymerase
DNA/RNA (5'-D(*AP*C)-R(P*A)-D(P*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')

Keywords

TRANSFERASE/DNA / RIBONUCLEOTIDE / TRANSFERASE-DNA complex

Function / homology

Function and homology information

bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function

Biological species

Enterobacteria phage RB69 (virus)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.12 Å

Authors

Clausen, A.R. / Pedersen, L.C.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
Authors: Clausen, A.R. / Murray, M.S. / Passer, A.R. / Pedersen, L.C. / Kunkel, T.A.

History

Deposition	May 1, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2013	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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_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_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_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	4khs.cif.gz	431.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4khs.ent.gz	344.6 KB	Display	PDB format
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Validation report

Summary document	4khs_validation.pdf.gz	800.5 KB	Display	wwPDB validaton report
Full document	4khs_full_validation.pdf.gz	805.6 KB	Display
Data in XML	4khs_validation.xml.gz	39.2 KB	Display
Data in CIF	4khs_validation.cif.gz	59.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kh/4khs ftp://data.pdbj.org/pub/pdb/validation_reports/kh/4khs	HTTPS FTP

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Related structure data

Related structure data	4khqC 4khuC 4khwC 4khyC 4ki4C 4ki6C C: citing same article (ref.)
Similar structure data	4khw-d 3lds-d 2ozs-d 4e3s-d 4ki6-d 3cq8-d 4dto-d 1ig9-d 3kd5-d 4m42-d 4khy-d 4m41-d 4m3r-d 4khq-d 3kd1-d 3sq4-d 3lzj-d 3sjj-d 3si6-d 3qet-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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #3 - Mar 2000 DNA Polymerase similarity (12) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #247 - Jul 2020 Myelin-associated Glycoprotein similarity (9) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (5) #238 - Oct 2019 Ribonucleotide Reductase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

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similarity (1)
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similarity (1)
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similarity (1)
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similarity (1)
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similarity (1)
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similarity (1)
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Deposited unit

A: DNA polymerase

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

T: DNA/RNA (5'-D(*AP*C)-R(P*A)-D(P*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')

hetero molecules

115 kDa, 3 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)	80.699, 119.572, 127.800
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 / DNA chain / DNA/RNA hybrid , 3 types, 3 molecules APT

#1: Protein	DNA polymerase / Gp43 Mass: 104689.156 Da / Num. of mol.: 1 / Mutation: D327A, D222A, L415F 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
#2: DNA chain	DNA (5'-D(GPCPGPGPAPCPTPGPCPTPTPAPCPC)-3') Mass: 4256.766 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA/RNA hybrid	DNA/RNA (5'-D(APC)-R(PA)-D(PGPGPTPAPAPGPCPAPGPTPCPCPGPCPG)-3') Mass: 5566.604 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 5 types, 673 molecules

#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical	ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₂O₁₄P₃
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 664 / 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: 2.69 Å³/Da / Density % sol: 54.31 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50 MM TRIS-HCL, 10% PEG350, 220 MM CALCIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K, pH 7.5, temperature 298K

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Data collection

Diffraction	Mean temperature: 95 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
Detector	Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 9, 2010
Radiation	Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. all: 66285 / Num. obs: 66285 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.1
Reflection shell	Resolution: 2.1→2.14 Å / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.7_650)	model building
PHENIX	(PHENIX.REFINE: 1.7_650)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.7_650	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.12→27.077 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 23.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2164	6358	9.71 %
R_work	0.1762	-	-
obs	0.1801	59378	98.25 %
all	-	66285	-

Solvent computation

Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.0341 Å²	-0 Å²	0 Å²
2-	-	-3.8511 Å²	0 Å²
3-	-	-	4.8851 Å²

Refinement step

Cycle: LAST / Resolution: 2.12→27.077 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7147	647	37	664	8495

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	8219
X-RAY DIFFRACTION	f_angle_d	0.815	11341
X-RAY DIFFRACTION	f_dihedral_angle_d	11.606	2741
X-RAY DIFFRACTION	f_chiral_restr	0.056	1200
X-RAY DIFFRACTION	f_plane_restr	0.003	1349

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 (%)
2.1203-2.1444	0.3084	123	0.2707	1100	X-RAY DIFFRACTION	52
2.1444-2.1696	0.3068	205	0.2554	2069	X-RAY DIFFRACTION	98
2.1696-2.196	0.3208	228	0.2384	2107	X-RAY DIFFRACTION	100
2.196-2.2238	0.2837	232	0.2455	2107	X-RAY DIFFRACTION	100
2.2238-2.2531	0.3219	244	0.2783	2075	X-RAY DIFFRACTION	100
2.2531-2.2839	0.2649	218	0.2385	2090	X-RAY DIFFRACTION	100
2.2839-2.3165	0.2729	214	0.225	2116	X-RAY DIFFRACTION	100
2.3165-2.3511	0.3316	224	0.2191	2109	X-RAY DIFFRACTION	100
2.3511-2.3878	0.2564	235	0.2045	2082	X-RAY DIFFRACTION	100
2.3878-2.4269	0.2972	237	0.1933	2097	X-RAY DIFFRACTION	100
2.4269-2.4687	0.2347	212	0.1934	2115	X-RAY DIFFRACTION	100
2.4687-2.5136	0.2285	223	0.1909	2123	X-RAY DIFFRACTION	100
2.5136-2.5619	0.2585	246	0.1954	2075	X-RAY DIFFRACTION	100
2.5619-2.6142	0.2603	201	0.1873	2161	X-RAY DIFFRACTION	100
2.6142-2.671	0.2528	248	0.1898	2093	X-RAY DIFFRACTION	100
2.671-2.733	0.2489	228	0.19	2091	X-RAY DIFFRACTION	100
2.733-2.8013	0.2725	225	0.1896	2144	X-RAY DIFFRACTION	100
2.8013-2.877	0.2335	230	0.193	2115	X-RAY DIFFRACTION	100
2.877-2.9615	0.2504	229	0.1948	2098	X-RAY DIFFRACTION	100
2.9615-3.057	0.2281	207	0.1967	2149	X-RAY DIFFRACTION	100
3.057-3.1661	0.2418	239	0.1966	2101	X-RAY DIFFRACTION	100
3.1661-3.2927	0.2407	263	0.1909	2113	X-RAY DIFFRACTION	100
3.2927-3.4422	0.2129	238	0.1748	2141	X-RAY DIFFRACTION	100
3.4422-3.6233	0.1911	244	0.1693	2114	X-RAY DIFFRACTION	100
3.6233-3.8497	0.1874	216	0.1611	2156	X-RAY DIFFRACTION	100
3.8497-4.146	0.1627	221	0.1418	2158	X-RAY DIFFRACTION	100
4.146-4.5614	0.1734	222	0.131	2173	X-RAY DIFFRACTION	100
4.5614-5.2174	0.156	241	0.1284	2171	X-RAY DIFFRACTION	100
5.2174-6.5579	0.1797	221	0.1606	2222	X-RAY DIFFRACTION	100
6.5579-27.0789	0.1988	235	0.1721	2294	X-RAY DIFFRACTION	99

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	0.6346	0.9886	-0.3643	2.6634	-0.8132	1.5878	0.0648	-0.0002	0.146	0.2063	-0.1382	-0.5914	-0.2263	0.1307	0.0415	0.2495	-0.003	-0.0054	0.327	0.0941	0.6324	28.7918	3.5496	-29.9981
2	1.0886	0.3467	-0.5103	2.6567	-0.6836	1.791	-0.0206	-0.0566	-0.0538	0.3673	-0.1734	-0.253	0.202	-0.1121	0.1333	0.2819	-0.0171	-0.0933	0.2586	0.0193	0.2641	12.6433	-28.8988	-11.2974
3	1.3561	0.598	-0.4963	1.8471	-0.0057	2.1216	0.1718	-0.2219	0.2011	0.4739	-0.1539	-0.4123	-0.2586	0.1769	0.0115	0.3344	-0.0209	-0.1323	0.2707	0.0234	0.317	16.7377	-14.0874	-10.5525
4	1.6852	-0.3959	0.7722	1.3658	0.5965	1.962	-0.0423	-0.0889	-0.0332	0.0034	0.0004	0.2718	0.251	-0.2779	0.0329	0.2717	0.0246	0.0084	0.2779	0.0277	0.2508	-0.0399	-24.3693	-24.1986
5	0.5899	0.1217	-0.0151	1.3116	-0.4114	0.7168	0.0275	0.0481	0.1375	-0.1793	-0.1058	-0.2093	0.1312	-0.0078	0.0252	0.2057	0.0272	0.0226	0.2189	0.0119	0.2054	7.4862	-13.4548	-35.0826
6	1.8329	0.4515	0.3394	1.992	-0.3093	1.4787	-0.0357	0.3379	-0.0912	-0.3442	-0.0154	-0.3881	0.4824	0.1986	-0.0076	0.4464	0.1195	0.1669	0.3349	0.0166	0.1275	8.9586	-17.2864	-52.33
7	1.0527	0.1975	-0.1399	1.6103	-0.552	0.8403	-0.0619	0.3908	0.0489	-0.7006	0.0412	0.0087	0.4858	-0.0522	0.0099	0.5857	0.0082	0.0098	0.3694	0.0379	0.1828	-0.4314	-13.2635	-57.151
8	1.6045	-0.5721	-0.1983	1.6759	0.1739	1.3239	-0.035	0.459	-0.1562	-0.3706	0.0011	-0.0122	0.5087	-0.0262	0.0486	0.642	-0.023	-0.0386	0.3434	-0.0141	0.2807	-10.0735	-25.3093	-53.0951
9	1.8186	-0.0569	0.0321	1.995	0.3626	2.6407	-0.0592	-0.3105	-0.0734	0.0875	0.0207	0.3075	0.1208	-0.1948	0.0292	0.1656	-0.0033	-0.0004	0.2263	0.0646	0.2601	-20.0561	-21.2635	-24.7602
10	1.9159	0.6295	0.4488	1.2576	0.0572	0.8029	-0.1577	0.3018	-0.193	-0.5607	-0.1793	0.2824	-0.074	-0.3469	0.229	0.3916	-0.0636	-0.1083	0.4538	0.0286	0.5052	-32.4797	-24.9877	-43.6907
11	5.8527	0.5576	-0.9743	1.4467	0.462	0.7662	-0.3061	0.108	-0.5197	-0.1952	0.2212	0.5091	0.8494	0.071	0.138	0.3517	0.0783	0.1255	0.8348	0.2626	1.2187	-35.6491	-1.7613	-34.0138
12	3.8707	-0.8376	1.2805	1.1051	0.4562	1.1417	-0.1771	0.8169	0.9871	0.4327	0.3272	-0.3444	-0.522	0.0302	0.0922	0.3076	0.0062	-0.055	0.4622	0.0862	0.8985	-19.8958	0.4518	-31.5909
13	1.0666	0.4434	-0.1942	1.0125	-0.8691	0.7828	-0.2557	0.1591	0.2766	-0.2355	0.0662	-0.1419	0.1551	-0.112	0.0444	0.2815	-0.0074	0.0309	0.2671	0.0431	0.2887	-9.1574	-11.1759	-37.1968
14	3.1213	-0.5452	0.1837	1.9241	-0.7367	0.4301	-0.1611	-0.4459	0.4579	0.0497	0.0297	-0.093	-0.1056	-0.0881	0.0627	0.2381	0.0442	0.0327	0.3176	0.0222	0.3242	-3.023	-2.7197	-37.9051
15	1.2493	-0.5132	-1.2606	1.2	0.7923	2.3753	-0.5366	0.1409	-0.0069	0.5205	0.1177	0.2905	0.428	-0.5255	0.0584	0.333	0.0326	0.0357	0.4284	-0.0042	0.5199	-23.078	-8.1723	-32.026
16	1.9511	0.8649	1.0483	0.3937	0.4996	0.4505	-1.0508	-0.0061	0.7367	0.358	0.2424	-0.1365	0.2175	0.4999	-0.6743	0.2682	0.2679	-0.0439	0.5337	0.1435	0.966	-37.3682	4.6542	-31.2232

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:98)
2	X-RAY DIFFRACTION	2	(chain A and resid 99:197)
3	X-RAY DIFFRACTION	3	(chain A and resid 198:270)
4	X-RAY DIFFRACTION	4	(chain A and resid 271:310)
5	X-RAY DIFFRACTION	5	(chain A and resid 311:416)
6	X-RAY DIFFRACTION	6	(chain A and resid 417:541)
7	X-RAY DIFFRACTION	7	(chain A and resid 542:683)
8	X-RAY DIFFRACTION	8	(chain A and resid 684:724)
9	X-RAY DIFFRACTION	9	(chain A and resid 725:870)
10	X-RAY DIFFRACTION	10	(chain A and resid 871:902)
11	X-RAY DIFFRACTION	11	(chain P and resid 102:106)
12	X-RAY DIFFRACTION	12	(chain P and resid 107:110)
13	X-RAY DIFFRACTION	13	(chain P and resid 111:115)
14	X-RAY DIFFRACTION	14	(chain T and resid 1:8)
15	X-RAY DIFFRACTION	15	(chain T and resid 9:12)
16	X-RAY DIFFRACTION	16	(chain T and resid 13:18)

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