PDB-6iod: The structure of UdgX in complex with single-stranded DNA

ID or keywords:

Entry

Database: PDB / ID: 6iod

Title

The structure of UdgX in complex with single-stranded DNA

Components

DNA
Phage SPO1 DNA polymerase-related protein

Keywords

DNA BINDING PROTEIN/DNA / uracil DNA glycosylase / DNA repair / iron-sulfur / DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

uracil DNA N-glycosylase activity / nucleotidyltransferase activity / 4 iron, 4 sulfur cluster binding / DNA repair / metal ion binding
Similarity search - Function

Biological species

Mycobacterium smegmatis MC2 155 (bacteria)

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.66 Å

Authors

Xie, W. / Tu, J.

Funding support

China, 2items

Citation

Journal: Nat.Chem.Biol. / Year: 2019
Title: Suicide inactivation of the uracil DNA glycosylase UdgX by covalent complex formation.
Authors: Tu, J. / Chen, R. / Yang, Y. / Cao, W. / Xie, W.

History

Deposition	Oct 29, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 31, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 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 / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6iod.cif.gz	194.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6iod.ent.gz	150.1 KB	Display	PDB format
PDBx/mmJSON format	6iod.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6iod_validation.pdf.gz	477.4 KB	Display	wwPDB validaton report
Full document	6iod_full_validation.pdf.gz	481.3 KB	Display
Data in XML	6iod_validation.xml.gz	20.8 KB	Display
Data in CIF	6iod_validation.cif.gz	30.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/io/6iod ftp://data.pdbj.org/pub/pdb/validation_reports/io/6iod	HTTPS FTP

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Related structure data

Related structure data	6io9SC 6ioaC 6iobC 6iocC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6l6s-1 4psu-d 4xde-d 2xbv-d 3pe6-d 4awn-d 5ar1-d 6ur0-1 6baw-2 6baw-1 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
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
similarity (1)
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#253 - Jan 2021
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#180 - Dec 2014
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#135 - Mar 2011
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similarity (1)
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Estrogen Receptor
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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Twenty Years of Molecules
similarity (1)

Deposited unit

A: Phage SPO1 DNA polymerase-related protein

B: Phage SPO1 DNA polymerase-related protein

C: DNA

D: DNA

hetero molecules

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

1

A: Phage SPO1 DNA polymerase-related protein

C: DNA

hetero molecules

defined by author&software
Evidence: gel filtration
27.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phage SPO1 DNA polymerase-related protein

D: DNA

hetero molecules

defined by author&software
27.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	43.805, 83.862, 122.664
Angle α, β, γ (deg.)	90.00, 94.51, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Phage SPO1 DNA polymerase-related protein Mass: 22483.561 Da / Num. of mol.: 2 / Fragment: UNP residues 7-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis MC2 155 (bacteria) Strain: MC2 155 / Gene: MSMEI_0259 / Production host: Escherichia coli (E. coli) / References: UniProt: I7F541, DNA-directed DNA polymerase
#2: DNA chain	DNA Mass: 4830.117 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mycobacterium smegmatis (bacteria)
#3: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.06 Å³/Da / Density % sol: 40.17 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 2.15M sodium malonate pH 7.0 and 3.8% MPD

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.66→50 Å / Num. obs: 52269 / % possible obs: 99.6 % / Observed criterion σ(I): 5.5 / Redundancy: 6.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.052 / Net I/σ(I): 33.1
Reflection shell	Resolution: 1.66→1.72 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.496 / Num. unique obs: 5176 / CC_1/2: 0.944 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6IO9

6io9

Resolution: 1.66→41.931 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.31

	R_factor	Num. reflection	% reflection
R_free	0.2169	2558	4.92 %
R_work	0.1822	-	-
obs	0.184	52033	99.49 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.66→41.931 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2963	460	16	322	3761

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3563
X-RAY DIFFRACTION	f_angle_d	1.633	4922
X-RAY DIFFRACTION	f_dihedral_angle_d	18.414	2017
X-RAY DIFFRACTION	f_chiral_restr	0.063	564
X-RAY DIFFRACTION	f_plane_restr	0.007	572

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 (%)
1.659-1.6909	0.212	143	0.2034	2771	X-RAY DIFFRACTION	99
1.6909-1.7255	0.2266	129	0.1883	2696	X-RAY DIFFRACTION	100
1.7255-1.763	0.2121	148	0.1918	2741	X-RAY DIFFRACTION	100
1.763-1.804	0.2152	122	0.1809	2762	X-RAY DIFFRACTION	99
1.804-1.8491	0.2129	125	0.1871	2734	X-RAY DIFFRACTION	99
1.8491-1.8991	0.1926	134	0.1803	2725	X-RAY DIFFRACTION	97
1.8991-1.955	0.2223	135	0.1897	2723	X-RAY DIFFRACTION	100
1.955-2.0181	0.2164	132	0.1867	2766	X-RAY DIFFRACTION	100
2.0181-2.0902	0.217	147	0.1848	2759	X-RAY DIFFRACTION	100
2.0902-2.1739	0.224	166	0.1846	2723	X-RAY DIFFRACTION	100
2.1739-2.2728	0.2013	147	0.1803	2732	X-RAY DIFFRACTION	100
2.2728-2.3926	0.2128	146	0.1876	2722	X-RAY DIFFRACTION	99
2.3926-2.5425	0.2184	148	0.1857	2748	X-RAY DIFFRACTION	100
2.5425-2.7388	0.2398	123	0.2053	2785	X-RAY DIFFRACTION	100
2.7388-3.0143	0.2323	146	0.1985	2751	X-RAY DIFFRACTION	100
3.0143-3.4504	0.2236	159	0.1795	2744	X-RAY DIFFRACTION	99
3.4504-4.3464	0.2173	158	0.1591	2788	X-RAY DIFFRACTION	100
4.3464-41.9444	0.2045	150	0.1701	2805	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	0.0346	0.0065	0.0177	0.0045	0.0052	0.0105	0.0403	-0.0519	-0.0307	-0.0018	0.0121	-0.0532	0.0217	0.041	0.0887	0.0581	-0.0075	-0.0185	0.0596	0.0165	0.0742	52.1414	-15.8244	266.7605
2	0.0228	-0.0062	0.0125	0.0062	-0.0076	0.0374	0.0386	-0.1572	-0.0421	0.0065	-0.0201	0.0239	-0.0632	-0.0339	0.0011	0.047	-0.0124	0.0022	0.04	0.004	0.0637	33.2643	-13.5041	266.9285
3	0.0093	-0.019	0.0067	0.0494	-0.0211	0.018	0.0227	-0.0598	-0.0201	-0.0218	0.0185	0.0443	-0.0705	-0.0291	0.0088	-0.0188	-0.1479	0.0397	-0.1955	0.0878	0.0577	37.6321	-12.8383	265.7817
4	0	-0.0016	-0.005	0.0201	0.0097	0.0167	0.0053	-0.0205	0.0172	0.0017	-0.0114	0.0061	-0.0124	0.0076	-0.0135	0.1013	-0.0273	0.025	-0.0386	0.004	0.0624	43.5936	2.0645	261.4876
5	0.0318	0.0319	0.0149	0.0539	0.0299	0.0281	0.0287	0.1241	-0.1536	-0.0646	0.0389	-0.061	0.0367	0.0972	0.0181	0.0624	0.0063	0.0005	0.0369	0.0118	0.0782	41.1348	-19.3616	255.1966
6	0.02	0.0045	0.0111	0.0133	-0.0154	0.0473	-0.0279	0.0559	-0.0183	-0.0304	0.0483	-0.0429	0.0104	-0.0416	0.0157	0.087	-0.0045	-0.0079	-0.1265	-0.0455	0.1029	28.3592	-18.0907	254.7798
7	0.0007	0.0003	0.0003	0.0007	-0.0018	0.002	0.005	-0.0027	0.0028	0.003	0.0062	-0.0063	0.0006	0.0021	0	0.3521	-0.0753	-0.0611	0.4826	0.0112	0.4046	44.295	0.2355	293.5781
8	0.0185	-0.0015	0.0042	0.0369	-0.0127	0.0436	0.0049	-0.1437	-0.0082	0.0143	-0.071	-0.0693	-0.0135	0.0903	-0.0279	0.0574	-0.0214	-0.0374	0.4088	0.0636	0.0652	36.0158	-8.4696	285.8565
9	0.0051	0.0037	-0.0079	0.0034	-0.0061	0.0131	0.0165	-0.0346	0.0098	-0.0268	-0.0097	-0.0063	-0.039	0.0314	0.0078	0.0959	-0.0118	0.004	0.1708	-0.0326	0.0691	24.3325	-4.0765	276.4611
10	0.0086	0.0029	-0.0083	0.0106	0.0022	0.0087	-0.005	-0.0239	-0.0272	0.0073	0.0018	-0.0016	0.0188	0.014	-0.0053	0.1586	-0.012	-0.025	0.4186	0.0997	0.1391	31.4651	-17.3259	292.1206
11	0.0089	0.002	0.0052	-0.0003	0.0035	0.0063	-0.0138	-0.0455	0.0172	0.032	-0.0318	-0.0117	-0.0226	0.0158	-0.028	0.196	-0.1595	0.0013	0.431	-0.1294	0.014	31.3149	-0.4334	292.4067
12	0.0164	-0.0068	-0.0028	0.0023	0.0016	0.0099	0.0169	0.0023	0.005	0.002	0.0085	0.0138	-0.0065	-0.0085	0.012	0.2066	-0.0761	0.0383	0.4469	-0.0923	0.0982	18.8778	-3.5973	297.4
13	0.0442	-0.0034	-0.0018	0.0042	-0.0163	0.0653	0.0632	-0.0213	0.0269	-0.001	0.0435	-0.0023	-0.0029	-0.0132	0.0399	0.1447	-0.02	0.0317	0.2687	-0.0452	0.1106	17.872	-3.291	288.8062
14	0.0472	-0.0244	0.0198	0.0533	-0.0357	0.0661	0.0431	-0.0485	0.0148	-0.012	0.0548	-0.0032	-0.0088	-0.0204	0.0281	0.1057	-0.0084	0.0035	0.1964	-0.0421	0.1097	12.7411	-3.8205	280.4449
15	0.008	0.0059	0.0005	0.0057	-0.0039	0.0004	-0.0102	-0.0102	0.0576	-0.0324	-0.019	-0.0466	-0.0343	-0.021	-0.0697	0.1044	-0.001	0.0087	0.0505	0.0037	0.0838	39.6145	-0.8202	248.8297
16	0.0001	-0.0026	-0.0003	0.0031	-0.0008	0.001	0.0122	-0.027	-0.0425	0.0536	-0.0049	0.0083	0.0401	0.0029	0	0.2047	-0.0336	0.0339	0.3089	0.0236	0.169	18.1705	-18.9089	297.6932

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 40 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 41 through 79 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 80 through 101 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 102 through 113 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 114 through 157 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 158 through 209 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 4 through 13 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 14 through 67 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 68 through 91 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 92 through 113 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 114 through 140 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 141 through 157 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 158 through 186 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 187 through 208 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 6 through 16 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 6 through 16 )

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