PDB-4ljr: Structural insights into the unique single-stranded DNA binding m...

ID or keywords:

Entry

Database: PDB / ID: 4ljr

Title

Structural insights into the unique single-stranded DNA binding mode of DNA processing protein A from Helicobacter pylori

Components

DNA processing chain A
single-stranded DNA

Keywords

DNA BINDING PROTEIN/DNA / DNA processing A domain / Rossmann fold / ssDNA binding / complex / natural recombination mediating protein / DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

DNA-mediated transformation
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Wang, W.

Citation

Journal: Nucleic Acids Res. / Year: 2014
Title: Structural insights into the unique single-stranded DNA-binding mode of Helicobacter pylori DprA.
Authors: Wang, W. / Ding, J. / Zhang, Y. / Hu, Y. / Wang, D.C.

History

Deposition	Jul 5, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 1, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 29, 2014	Group: Database references
Revision 1.2	Apr 2, 2014	Group: Database references
Revision 1.3	Nov 12, 2014	Group: Structure summary
Revision 1.4	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_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ljr.cif.gz	195.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4ljr.ent.gz	154.9 KB	Display	PDB format
PDBx/mmJSON format	4ljr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ljr_validation.pdf.gz	442.1 KB	Display	wwPDB validaton report
Full document	4ljr_full_validation.pdf.gz	444.2 KB	Display
Data in XML	4ljr_validation.xml.gz	21.4 KB	Display
Data in CIF	4ljr_validation.cif.gz	31.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lj/4ljr ftp://data.pdbj.org/pub/pdb/validation_reports/lj/4ljr	HTTPS FTP

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Related structure data

Related structure data	4ljkC 4ljlSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4ljk-3 4q9v-d 4ljk-4 4ljl-d 6bqk-d 4exb-2 3zik-1 4ljk-1 4xu1-d 4exa-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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #253 - Jan 2021 Expressome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #227 - Nov 2018 Telomerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #135 - Mar 2011 Integrase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #23 - Nov 2001 DNA similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
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Thymine Dimers
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#168 - Dec 2013
DNA Helicase
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#253 - Jan 2021
Expressome
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#172 - Apr 2014
RecA and Rad51
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#122 - Feb 2010
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similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#40 - Apr 2003
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similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
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Zinc Fingers
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#119 - Nov 2009
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similarity (1)
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Hypoxia-Inducible Factors
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Twenty Years of Molecules
similarity (1)

Deposited unit

A: DNA processing chain A

B: DNA processing chain A

C: single-stranded DNA

D: single-stranded DNA

70.6 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)	37.400, 40.510, 154.680
Angle α, β, γ (deg.)	90.00, 92.18, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	DNA processing chain A Mass: 24692.584 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP0333, HP_0333 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O25100
#2: DNA chain	single-stranded DNA Mass: 10601.791 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 385 / 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 grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 15% PEG3350, 100 mM NaAc, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→40.51 Å / Num. all: 43477 / Num. obs: 36291 / % possible obs: 83.6 %

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASES		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LJL

4ljl

Resolution: 1.8→33.155 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 24.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2371	1759	5.03 %	Random
R_work	0.194	-	-	-
obs	0.1962	34988	80.5 %	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.5 Å² / k_sol: 0.348 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.7783 Å²	-0 Å²	1.3559 Å²
2-	-	7.0078 Å²	0 Å²
3-	-	-	-4.2295 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→33.155 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3318	142	0	385	3845

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3530
X-RAY DIFFRACTION	f_angle_d	0.87	4804
X-RAY DIFFRACTION	f_dihedral_angle_d	13.933	1360
X-RAY DIFFRACTION	f_chiral_restr	0.059	564
X-RAY DIFFRACTION	f_plane_restr	0.004	593

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 (%)
1.8-1.8487	0.3342	111	0.2683	2275	X-RAY DIFFRACTION	71
1.8487-1.9031	0.2936	108	0.2564	2098	X-RAY DIFFRACTION	67
1.9031-1.9645	0.4481	111	0.3552	2000	X-RAY DIFFRACTION	64
1.9645-2.0347	0.2753	122	0.2092	2397	X-RAY DIFFRACTION	76
2.0347-2.1162	0.244	132	0.1992	2423	X-RAY DIFFRACTION	77
2.1162-2.2125	0.2382	118	0.1938	2469	X-RAY DIFFRACTION	78
2.2125-2.3291	0.3759	103	0.2712	2044	X-RAY DIFFRACTION	65
2.3291-2.475	0.214	120	0.1896	2647	X-RAY DIFFRACTION	83
2.475-2.666	0.2463	172	0.2006	2831	X-RAY DIFFRACTION	89
2.666-2.9341	0.2589	159	0.1971	2931	X-RAY DIFFRACTION	93
2.9341-3.3583	0.2389	172	0.1857	3049	X-RAY DIFFRACTION	96
3.3583-4.2298	0.1816	175	0.1576	3051	X-RAY DIFFRACTION	95
4.2298-33.1604	0.1985	156	0.1711	3014	X-RAY DIFFRACTION	91

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	0.4476	0.256	0.0526	0.427	-0.1123	0.3704	0.0444	-0.0082	-0.1419	-0.0068	-0.1342	-0.1252	0.0965	-0.1158	0.0011	0.1151	0.0099	-0.0037	0.1092	-0.036	0.167	18.7643	-8.0199	2.4677
2	0.1479	-0.0931	-0.3887	0.2112	0.1736	1.1938	0.0043	0.1941	-0.0812	-0.0862	-0.1223	-0.0131	0.1404	-0.4792	0.0063	0.1211	-0.0099	0.0088	0.0936	-0.0324	0.1926	7.3728	-5.8618	6.2797
3	0.7097	0.0299	0.2955	0.3773	0.2786	0.3264	-0.0893	-0.6978	-0.0024	0.2098	-0.0133	0.1053	0.116	0.1369	-0.0048	0.2094	-0.0146	-0.0344	0.398	0.0103	0.1409	16.3744	-4.663	27.4294
4	0.2958	0.0549	0.0752	0.1317	0.0095	0.2141	-0.0189	-0.2066	0.0619	-0.0378	-0.0736	-0.0457	0.0647	0.0468	-0.0263	0.0906	0.0011	-0.0167	0.1041	-0.0141	0.1115	19.3208	-4.8264	16.0887
5	0.7367	-0.2925	-0.3939	0.4393	-0.3388	1.0068	-0.1609	-0.2248	-0.3476	-0.1202	-0.0188	-0.198	0.359	0.4254	0.0759	0.1213	0.0186	-0.0204	0.2102	0.0331	0.2172	26.7858	-7.8129	14.1504
6	0.087	-0.1424	0.0077	0.2815	0.0112	0.0921	-0.0658	0.194	-0.022	-0.2177	-0.0668	-0.1236	0.0659	0.238	-0.0342	0.1036	0.0526	-0.0047	-0.3573	0.0312	0.224	18.5746	0.363	3.6128
7	0.2114	-0.0234	0.3153	0.4545	0.1567	0.636	-0.0005	-0.4587	0.1757	-0.0299	-0.116	0.0018	-0.0474	-0.4865	0.0455	0.1294	0.0481	-0.0246	0.1022	-0.1042	0.2003	11.4373	4.4069	18.0184
8	0.3545	0.1959	0.2314	0.4141	-0.0019	0.2988	0.0636	-0.3261	0.2029	-0.1299	-0.0738	0.1977	-0.0571	0.1189	0.0146	0.1985	0.0296	-0.0478	0.2954	-0.1154	0.2042	4.6217	4.7229	22.3252
9	0.1221	-0.0221	-0.004	0.0346	0.0063	0.0301	-0.0056	0.035	0.1004	-0.0688	-0.0113	0.0177	-0.1571	-0.0332	0.0567	0.2877	0.1202	0.0187	0.605	-0.5059	-0.1622	11.5667	9.8239	34.7415
10	0.6456	0.3225	0.3893	0.9255	0.2596	0.4967	0.0115	-0.8087	-0.1287	0.4731	-0.1987	0.1387	0.2051	-0.333	0.003	0.2051	-0.0426	0.1071	0.5807	0.0844	0.1792	4.5931	-5.695	32.798
11	0.7953	-0.1343	-0.0152	0.3993	-0.0197	0.4034	0.0297	-0.0926	0.1125	0.2209	-0.091	0.1439	-0.062	-0.0539	0.0288	0.2242	-0.0048	0.0305	0.1443	-0.0467	0.1858	5.3099	17.7433	77.1581
12	0.1951	0.0998	-0.232	1.0093	-0.0853	0.723	0.0989	0.1772	0.0155	0.1206	-0.1505	0.4703	-0.0681	-0.4823	0.0604	0.1324	0.015	0.0379	0.2669	-0.0611	0.2947	-3.7325	15.7987	69.4853
13	0.4095	0.2265	0.1359	0.3207	0.2321	0.1732	-0.1167	0.4963	0.072	-0.1565	0.1528	-0.089	-0.2028	0.126	-0.0379	0.2196	0.0571	0.0294	0.2863	-0.0229	0.1026	11.9252	15.589	52.8251
14	0.6048	-0.2974	-0.135	0.7493	0.3205	0.7702	-0.0095	0.065	-0.0873	0.0422	-0.0431	0.0604	0.0095	0.0018	0.0156	0.1634	0.0019	0.0249	0.1416	-0.0255	0.1552	9.3669	13.0311	67.4689
15	0.5237	-0.0788	0.2538	0.3699	-0.3235	0.3705	-0.2338	0.3464	-0.2324	0.0818	-0.2273	0.2848	0.1395	-0.4121	0.0768	0.2788	-0.0383	0.0622	0.4085	-0.1544	0.2926	1.9312	5.9726	53.5137
16	0.3812	-0.2537	0.0052	0.6069	-0.1021	0.0289	0.0626	-0.0563	-0.1421	0.1714	-0.0175	0.2155	0.2963	0.1258	0.0654	0.3428	0.0277	0.03	0.6506	-0.2268	0.2108	10.1213	1.1329	44.1097
17	0.402	-0.0528	-0.0304	0.262	-0.0206	0.0128	-0.0191	0.6027	0.0824	-0.3062	-0.153	0.0963	-0.1916	-0.1545	0.0413	0.4869	0.0979	-0.1306	0.6861	-0.0422	0.161	2.4817	16.7135	43.7065
18	0.0709	-0.159	-0.1285	0.5468	-0.0943	0.8408	0.0285	0.307	-0.29	-0.1424	-0.3033	0.1548	0.1992	0.1124	0.1142	0.4442	0.0785	0.0012	0.3396	-0.0165	0.2877	16.2698	-2.6786	65.9996
19	0.1714	0.0638	-0.1997	0.2988	0.2828	0.7235	-0.0126	-0.0108	0.0605	-0.0343	-0.0241	-0.0272	-0.0556	0.001	0.0135	1.4381	-0.2622	-0.0064	1.0847	-0.2711	0.8295	21.6497	10.383	13.4934

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 5:18)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 19:41)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 42:71)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 72:109)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 110:122)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 123:136)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 137:163)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 164:182)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 183:197)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 198:217)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 5:18)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 19:41)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 42:71)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 72:150)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 151:182)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 183:197)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 198:217)
18	X-RAY DIFFRACTION	18	chain 'C'
19	X-RAY DIFFRACTION	19	chain 'D'

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Yorodumi