PDB-6p0d: Human DNA Ligase 1 (E346A/E592A) Bound to an Adenylated, hydroxyl...

ID or keywords:

Entry

Database: PDB / ID: 6p0d

Title

Human DNA Ligase 1 (E346A/E592A) Bound to an Adenylated, hydroxyl terminated DNA nick

Components

DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')
DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')
DNA ligase 1

Keywords

LIGASE / protein-DNA complex / phosphotransferase / OB fold / DNA Binding domain / Adenylation Domain / metalloenzyme

Function / homology

Function and homology information

Okazaki fragment processing involved in mitotic DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / Processive synthesis on the lagging strand / lagging strand elongation / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Processive synthesis on the C-strand of the telomere ...
Similarity search - Function

Biological species

Homo sapiens (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Schellenberg, M.J. / Williams, R.S. / Tumbale, P.S. / Riccio, A.A.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2019
Title: Two-tiered enforcement of high-fidelity DNA ligation.
Authors: Tumbale, P.P. / Jurkiw, T.J. / Schellenberg, M.J. / Riccio, A.A. / O'Brien, P.J. / Williams, R.S.

History

Deposition	May 16, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2019	Provider: repository / Type: Initial release
Revision 1.1	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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Download

PDBx/mmCIF format	6p0d.cif.gz	462.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6p0d.ent.gz	373.6 KB	Display	PDB format
PDBx/mmJSON format	6p0d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6p0d_validation.pdf.gz	789.4 KB	Display	wwPDB validaton report
Full document	6p0d_full_validation.pdf.gz	793.7 KB	Display
Data in XML	6p0d_validation.xml.gz	35.4 KB	Display
Data in CIF	6p0d_validation.cif.gz	56.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p0/6p0d ftp://data.pdbj.org/pub/pdb/validation_reports/p0/6p0d	HTTPS FTP

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Related structure data

Related structure data	6p09C 6p0aC 6p0bC 6p0cC 6p0eC 6q1vC 1x9nS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7l34-d 6p0c-d 6p09-d 7kr3-d 6p0b-d 6p0a-d 6p0e-d 6q1v-d 7kr4-d 2b3y-2 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) #255 - Mar 2021 Cisplatin and DNA similarity (2) #168 - Dec 2013 DNA Helicase similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #55 - Jul 2004 DNA Ligase similarity (15) #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) #150 - Jun 2012 Sliding Clamps similarity (9) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase 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) #3 - Mar 2000 DNA Polymerase similarity (3) #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) #33 - Sep 2002 HIV Reverse Transcriptase similarity (2) #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) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #6 - Jun 2000 HIV-1 Protease similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: DNA ligase 1

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

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

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

hetero molecules

83.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

Unit cell

Length a, b, c (Å)	71.793, 101.227, 115.368
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 , 1 types, 1 molecules A

#1: Protein	DNA ligase 1 / DNA ligase I / Polydeoxyribonucleotide synthase [ATP] 1 Mass: 71669.938 Da / Num. of mol.: 1 / Mutation: E346A, E592A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LIG1 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18858, DNA ligase (ATP)

#1: Protein

DNA ligase 1 / DNA ligase I / Polydeoxyribonucleotide synthase [ATP] 1

Mass: 71669.938 Da / Num. of mol.: 1 / Mutation: E346A, E592A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: LIG1 / Plasmid: pMCSG7 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18858, DNA ligase (ATP)

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DNA chain , 3 types, 3 molecules BCD

#2: DNA chain	DNA (5'-D(GPCPTPGPAPTPGPCPGPTPC)-3') Mass: 3365.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source*: (synth.) synthetic construct (others)
#3: DNA chain	DNA (5'-D(PGPTPCPGPGPAPC)-3') Mass: 2138.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source*: (synth.) synthetic construct (others)
#4: DNA chain	DNA (5'-D(GPTPCPCPGPAPCPGPAPCPGPCPAPTPCPAPGPC)-3') Mass: 5486.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 972 molecules

#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 970 / 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: 2.53 Å³/Da / Density % sol: 51.43 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES, 100 mM Lithium Acetate, 15% (w/v) PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 8, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.75→50 Å / Num. obs: 86232 / % possible obs: 99.2 % / Redundancy: 5.9 % / B_iso Wilson estimate: 24.41 Å² / R_merge(I) obs: 0.104 / R_pim(I) all: 0.047 / R_rim(I) all: 0.114 / Χ²: 1.019 / Net I/σ(I): 7.8 / Num. measured all: 510358

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.75-1.81	3.4	1.016	8077	0.408	0.626	1.201	0.966	93.9
1.81-1.89	4.6	0.748	8571	0.681	0.39	0.847	1.024	100
1.89-1.97	6.3	0.554	8580	0.887	0.237	0.604	1.044	100
1.97-2.07	6.6	0.363	8610	0.95	0.152	0.394	1.064	100
2.07-2.2	6.6	0.245	8648	0.975	0.102	0.266	1.035	100
2.2-2.38	6.6	0.17	8641	0.987	0.071	0.185	0.994	100
2.38-2.61	6.6	0.13	8670	0.99	0.055	0.141	1.008	100
2.61-2.99	6.6	0.091	8722	0.994	0.038	0.099	1.015	100
2.99-3.77	6.4	0.073	8765	0.994	0.033	0.081	1.008	99.7
3.77-50	5.3	0.064	8948	0.989	0.032	0.072	1.001	98.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155)	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.25	data extraction
PHENIX		phasing
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1X9N

1x9n

Resolution: 1.75→34.276 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.91

	R_factor	Num. reflection	% reflection
R_free	0.1787	4327	5.03 %
R_work	0.1595	-	-
obs	0.1605	86108	99.04 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.75→34.276 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5008	733	29	970	6740

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6155
X-RAY DIFFRACTION	f_angle_d	0.706	8535
X-RAY DIFFRACTION	f_dihedral_angle_d	16.393	3688
X-RAY DIFFRACTION	f_chiral_restr	0.045	965
X-RAY DIFFRACTION	f_plane_restr	0.004	976

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 (%)
1.75-1.7588	0.3046	108	0.3049	2129	X-RAY DIFFRACTION	78
1.7588-1.7795	0.2586	143	0.2751	2718	X-RAY DIFFRACTION	100
1.7795-1.8012	0.3011	146	0.2627	2706	X-RAY DIFFRACTION	99
1.8012-1.824	0.2757	144	0.2507	2698	X-RAY DIFFRACTION	100
1.824-1.848	0.275	144	0.2254	2727	X-RAY DIFFRACTION	100
1.848-1.8733	0.2382	144	0.2164	2709	X-RAY DIFFRACTION	100
1.8733-1.9001	0.2152	142	0.2056	2727	X-RAY DIFFRACTION	100
1.9001-1.9285	0.2311	142	0.2032	2714	X-RAY DIFFRACTION	100
1.9285-1.9586	0.2524	144	0.1967	2732	X-RAY DIFFRACTION	100
1.9586-1.9907	0.224	146	0.1926	2724	X-RAY DIFFRACTION	100
1.9907-2.025	0.2377	146	0.191	2730	X-RAY DIFFRACTION	100
2.025-2.0618	0.1866	140	0.1736	2750	X-RAY DIFFRACTION	100
2.0618-2.1015	0.189	150	0.1682	2735	X-RAY DIFFRACTION	100
2.1015-2.1444	0.2131	144	0.1616	2726	X-RAY DIFFRACTION	100
2.1444-2.191	0.1908	145	0.1655	2739	X-RAY DIFFRACTION	100
2.191-2.2419	0.1922	133	0.1572	2732	X-RAY DIFFRACTION	100
2.2419-2.298	0.1968	116	0.1529	2776	X-RAY DIFFRACTION	100
2.298-2.3601	0.167	144	0.1553	2741	X-RAY DIFFRACTION	100
2.3601-2.4296	0.1968	150	0.1565	2711	X-RAY DIFFRACTION	100
2.4296-2.5079	0.1862	161	0.1609	2740	X-RAY DIFFRACTION	100
2.5079-2.5976	0.1985	146	0.1554	2767	X-RAY DIFFRACTION	100
2.5976-2.7015	0.1612	131	0.1562	2757	X-RAY DIFFRACTION	100
2.7015-2.8244	0.1857	143	0.1551	2773	X-RAY DIFFRACTION	100
2.8244-2.9732	0.1867	168	0.1611	2752	X-RAY DIFFRACTION	100
2.9732-3.1594	0.1608	134	0.1637	2765	X-RAY DIFFRACTION	100
3.1594-3.4031	0.1556	153	0.1451	2756	X-RAY DIFFRACTION	99
3.4031-3.7452	0.1357	149	0.136	2790	X-RAY DIFFRACTION	100
3.7452-4.2863	0.1532	151	0.1294	2790	X-RAY DIFFRACTION	99
4.2863-5.3969	0.1471	174	0.1274	2772	X-RAY DIFFRACTION	99
5.3969-34.2823	0.1726	146	0.1644	2895	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	1.6589	0.1865	-0.4236	1.0342	0.033	1.9744	0.083	-0.077	0.2907	0.0493	-0.0139	0.0177	-0.1681	-0.0424	-0.0984	0.1766	-0.0109	0.0057	0.1659	-0.0282	0.2383	32.9493	12.0831	-11.1028
2	0.9555	0.3233	-0.2872	1.0258	-0.1391	1.2698	-0.0199	-0.0477	0.0565	0.0413	0.0036	-0.0986	0.0026	0.1146	0.0061	0.1406	-0.0002	-0.0007	0.1835	0.0118	0.2076	36.5736	2.6221	-13.9962
3	1.6175	-0.4584	-0.1787	1.6866	0.4795	1.8261	-0.0512	0.0526	-0.0722	-0.0393	0.0046	0.106	0.0431	-0.1686	0.0434	0.1826	0.0009	0.0124	0.1425	-0.0015	0.1611	16.127	-22.5957	-16.2667
4	2.0206	-0.3125	-0.605	1.8252	0.3368	1.5962	0.0237	-0.0269	0.1549	0.1305	-0.0226	0.3104	-0.0255	-0.199	0.0111	0.1509	0.0168	0.0101	0.1848	0.0021	0.2097	-3.0542	2.4925	-6.7227
5	0.3625	0.2067	1.2804	0.1619	0.9488	5.6052	0.271	-0.207	0.0664	0.1111	0.2394	-0.246	-0.3018	-0.1812	-0.4946	0.3118	0.0573	0.0323	0.3215	-0.0471	0.2383	16.5588	-5.3563	5.5426
6	3.0331	0.9947	-1.3625	1.6156	-0.9155	3.8765	-0.0192	0.2518	0.1491	-0.0611	0.08	0.0509	0.0642	0.1479	-0.0599	0.1647	0.0137	-0.0016	0.218	0.0149	0.177	11.77	2.8737	-21.0801
7	2.0171	0.6958	-1.937	1.0407	-0.8914	2.8266	0.0344	0.0491	0.1557	-0.0451	0.119	0.1175	0.127	0.0322	-0.1409	0.1591	0.0163	-0.0192	0.1896	-0.0013	0.1726	14.262	0.6737	-15.0712
8	0.0969	0.4445	-0.0161	3.0795	1.0986	2.5457	0.0527	-0.0453	-0.0179	0.0129	0.2274	-0.2923	-0.5394	0.2269	-0.2018	0.373	0.0362	0.0222	0.3296	-0.0391	0.1825	17.9116	-8.2292	7.3495
9	3.7592	0.7737	0.3521	6.6921	-1.3773	4.1538	0.0554	-0.1284	0.4966	-0.4117	0.2505	0.101	-0.262	-0.3598	-0.2387	0.3979	0.0579	0.0142	0.3647	-0.0405	0.2475	19.5506	1.5274	19.6013

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 261 through 385 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 386 through 544 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 545 through 741 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 742 through 901 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 3 through 13 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 1 through 7 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 9 through 18 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 19 through 23 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 24 through 26 )

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Protein , 1 types, 1 molecules A

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DNA chain , 3 types, 3 molecules BCD

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Non-polymers , 3 types, 972 molecules

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-Protein , 1 types, 1 molecules A

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-Non-polymers , 3 types, 972 molecules

-Experimental details

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Protein , 1 types, 1 molecules A

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DNA chain , 3 types, 3 molecules BCD

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Non-polymers , 3 types, 972 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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