PDB-4pd2: Crystal structure of a complex between a C248GH LlFpg mutant and ...

ID or keywords:

Entry

Database: PDB / ID: 4pd2

Title

Crystal structure of a complex between a C248GH LlFpg mutant and a THF containing DNA

Components

DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3')
DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')
Formamidopyrimidine-DNA glycosylase

Keywords

Hydrolase/DNA / DNA GLYCOSYLASE / Hydrolase-DNA complex

Function / homology

Function and homology information

DNA-formamidopyrimidine glycosylase / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding
Similarity search - Function

Biological species

Lactococcus lactis subsp. cremoris (lactic acid bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Coste, F. / Castaing, B.

Citation

Journal: Nucleic Acids Res. / Year: 2014
Title: Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization.
Authors: Biela, A. / Coste, F. / Culard, F. / Guerin, M. / Goffinont, S. / Gasteiger, K. / Ciesla, J. / Winczura, A. / Kazimierczuk, Z. / Gasparutto, D. / Carell, T. / Tudek, B. / Castaing, B.

History

Deposition	Apr 17, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 1, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_conn / struct_conn_type Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4pd2.cif.gz	165.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4pd2.ent.gz	125.8 KB	Display	PDB format
PDBx/mmJSON format	4pd2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4pd2_validation.pdf.gz	437.5 KB	Display	wwPDB validaton report
Full document	4pd2_full_validation.pdf.gz	438.1 KB	Display
Data in XML	4pd2_validation.xml.gz	16.9 KB	Display
Data in CIF	4pd2_validation.cif.gz	26.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pd/4pd2 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/4pd2	HTTPS FTP

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Related structure data

Related structure data	4pczC 4pdgC 4pdiC 1pm5S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6rnr-d 6rp7-d 6ro2-d 4pdg-d 6h0s-d 6fl1-d 1tdz-d 6rok-d 1nnj-d 1pjj-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) #91 - Jul 2007 Thymine Dimers similarity (2) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA 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) #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) #3 - Mar 2000 DNA Polymerase 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) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (2)

PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Formamidopyrimidine-DNA glycosylase

B: DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3')

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

hetero molecules

39.7 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)	91.456, 91.456, 140.389
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-684- HOH

#1: Protein	Formamidopyrimidine-DNA glycosylase / Fapy-DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase MutM / AP lyase MutM Mass: 31208.271 Da / Num. of mol.: 1 / Mutation: C248GH Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria) Gene: mutM, fpg / Production host: Escherichia coli (E. coli) References: UniProt: P42371, DNA-formamidopyrimidine glycosylase
#2: DNA chain	DNA (5'-D(CPTPCPTPTPTP(3DR)PTPTPTPCPTPCPG)-3') Mass: 4054.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain	DNA (5'-D(GPCPGPAPGPAPAPAPCPAPAPAPGPA)-3') Mass: 4355.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.72 Å³/Da / Density % sol: 66.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES, SODIUM CITRATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.984 Å / Relative weight: 1
Reflection	Resolution: 1.65→47.56 Å / Num. obs: 70733 / % possible obs: 96.1 % / Redundancy: 4.9 % / R_merge(I) obs: 0.058 / Net I/σ(I): 14.2
Reflection shell	Resolution: 1.65→1.74 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.705 / Mean I/σ(I) obs: 2.2 / % possible all: 96.4

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1PM5

1pm5

Resolution: 1.65→45.728 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 18.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1789	6837	5.07 %	Random selection
R_work	0.1525	-	-	-
obs	0.1538	134864	98.5 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.65→45.728 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2149	557	1	368	3075

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	2840
X-RAY DIFFRACTION	f_angle_d	1.68	3949
X-RAY DIFFRACTION	f_dihedral_angle_d	19.18	1122
X-RAY DIFFRACTION	f_chiral_restr	0.093	445
X-RAY DIFFRACTION	f_plane_restr	0.009	407

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 (%)
1.65-1.6688	0.353	215	0.3027	4355	X-RAY DIFFRACTION	100
1.6688-1.6884	0.2704	246	0.2821	4309	X-RAY DIFFRACTION	100
1.6884-1.709	0.2998	243	0.2523	4307	X-RAY DIFFRACTION	100
1.709-1.7306	0.2795	221	0.2438	4292	X-RAY DIFFRACTION	100
1.7306-1.7534	0.2608	210	0.2388	4340	X-RAY DIFFRACTION	99
1.7534-1.7774	0.257	246	0.241	4275	X-RAY DIFFRACTION	99
1.7774-1.8028	0.2382	242	0.2327	4322	X-RAY DIFFRACTION	99
1.8028-1.8297	0.2288	243	0.2188	4317	X-RAY DIFFRACTION	99
1.8297-1.8583	0.2169	227	0.2003	4303	X-RAY DIFFRACTION	99
1.8583-1.8888	0.1909	230	0.1828	4268	X-RAY DIFFRACTION	99
1.8888-1.9214	0.2206	231	0.1737	4285	X-RAY DIFFRACTION	99
1.9214-1.9563	0.1896	236	0.1599	4314	X-RAY DIFFRACTION	99
1.9563-1.9939	0.1857	208	0.1576	4318	X-RAY DIFFRACTION	99
1.9939-2.0346	0.1703	250	0.152	4297	X-RAY DIFFRACTION	99
2.0346-2.0789	0.186	238	0.1622	4256	X-RAY DIFFRACTION	99
2.0789-2.1272	0.1781	247	0.1575	4284	X-RAY DIFFRACTION	99
2.1272-2.1804	0.1971	224	0.148	4268	X-RAY DIFFRACTION	99
2.1804-2.2394	0.1622	227	0.1416	4281	X-RAY DIFFRACTION	99
2.2394-2.3053	0.1988	224	0.1488	4250	X-RAY DIFFRACTION	99
2.3053-2.3797	0.1709	208	0.1547	4303	X-RAY DIFFRACTION	99
2.3797-2.4647	0.1963	199	0.1528	4284	X-RAY DIFFRACTION	98
2.4647-2.5634	0.2026	227	0.1594	4252	X-RAY DIFFRACTION	98
2.5634-2.68	0.2027	247	0.1701	4247	X-RAY DIFFRACTION	98
2.68-2.8213	0.2229	226	0.1742	4221	X-RAY DIFFRACTION	98
2.8213-2.998	0.1882	192	0.1699	4263	X-RAY DIFFRACTION	98
2.998-3.2295	0.1846	245	0.1508	4200	X-RAY DIFFRACTION	97
3.2295-3.5544	0.1733	258	0.1297	4162	X-RAY DIFFRACTION	97
3.5544-4.0684	0.1374	221	0.1222	4187	X-RAY DIFFRACTION	96
4.0684-5.1247	0.1238	224	0.1041	4133	X-RAY DIFFRACTION	96
5.1247-45.7455	0.1398	182	0.138	4134	X-RAY DIFFRACTION	94

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	0.2683	-0.1606	-0.0272	0.0994	-0.0408	0.2265	-0.1295	0.0763	-0.2656	-0.1482	0.0765	-0.2665	0.0451	0.2008	-0.0002	0.2158	0.0162	0.0302	0.2188	-0.0007	0.3196	-2.1554	1.3795	-15.4925
2	0.118	0.0519	0.0084	0.0999	0.0094	0.2821	-0.0274	-0.2307	-0.1318	0.2152	-0.0209	0.2452	-0.0109	-0.1907	0.0003	0.1997	0.009	0.0083	0.3032	0.0143	0.2701	-18.5638	8.7216	-6.3029
3	0.2012	-0.1203	0.1622	0.1673	-0.1922	0.193	-0.0651	0.1518	-0.2324	-0.2136	0.0958	0.1791	0.0869	-0.1793	0.0035	0.1853	-0.0402	-0.0145	0.2241	0.0086	0.3194	-16.1445	1.8708	-15.6597
4	0.5261	-0.3636	-0.4434	0.3813	0.0677	0.635	-0.0382	0.0358	-0.231	-0.0533	0.0043	-0.1839	0.1185	-0.0389	-0	0.1704	-0.0316	-0.0172	0.2105	-0.0106	0.1977	-9.9056	6.514	-14.3485
5	0.0237	0.021	-0.0386	0.0178	-0.0355	0.0572	0.0262	-0.0399	-0.1172	0.3216	0.0091	0.2798	-0.0003	0.0426	-0.0001	0.274	0.0032	-0.0161	0.2487	0.0401	0.2613	-9.6991	5.7954	0.8444
6	0.8721	-0.0292	-0.3928	0.6932	0.0698	0.2745	0.0203	0.0747	-0.1557	-0.0111	-0.0078	-0.0067	0.0173	-0.0901	0	0.1778	-0.0073	-0.019	0.246	-0.0144	0.2038	-10.5561	9.9377	-17.9621
7	-0.0091	0.0078	0.0137	0.0908	0.1429	0.2164	-0.1192	0.1595	-0.0843	-0.298	0.0279	0.0491	-0.0893	-0.1937	-0	0.2746	-0.06	-0.0148	0.3147	-0.0237	0.2312	2.2044	18.8452	-38.8139
8	0.5992	0.4862	0.2921	0.4784	0.0268	0.9297	-0.0496	-0.0051	0.0331	-0.0404	0.0654	-0.0461	-0.1323	0.1321	0	0.1857	-0.0284	0.0084	0.2438	-0.0299	0.2111	8.3688	21.5146	-29.2645
9	0.1078	-0.0574	-0.0053	0.0497	-0.0329	0.0451	-0.1062	0.0358	-0.4795	0.0913	-0.0151	-0.1155	0.1464	0.163	-0.0005	0.2157	-0.0016	0.021	0.3006	0.0052	0.3447	9.5772	6.6561	-21.7156
10	0.0045	0.0051	0.0055	0.0029	0.0053	0.0057	-0.2106	-0.0542	-0.1894	0.1854	-0.0907	-0.087	-0.4127	0.1282	-0.0005	0.5535	0.0341	-0.0358	0.7574	0.0393	0.4963	5.5878	6.086	-6.7878
11	0.1825	0.0805	0.1359	0.0278	0.0587	0.1142	0.0819	-0.3332	-0.2727	0.2438	-0.0669	-0.1845	0.0697	0.2327	0.0003	0.199	-0.0242	-0.0231	0.362	0.0162	0.3114	18.5245	16.1052	-16.1441
12	0.3217	0.2313	0.1543	0.2366	0.0235	0.1401	0.0025	-0.0174	0.0095	0.0266	0.0079	-0.0213	-0.1943	0.1972	0.0012	0.1765	-0.0541	0.0046	0.2916	-0.0284	0.2242	17.2018	26.9417	-20.7348
13	0.0058	-0.0033	0.0074	0.9259	0.0541	0.0049	0.0325	-0.3062	0.1543	-0.1921	-0.0267	-0.4161	-0.3689	0.0144	-0.0917	0.2724	-0.0467	-0.0368	0.4062	-0.1332	0.278	3.016	29.7597	-4.9365
14	0.0317	0.0251	-0.0731	0.0569	-0.0647	0.0863	0.3314	0.3007	-0.0892	-0.4032	-0.4272	1.481	-0.2798	0.2393	-0	0.3451	0.0214	-0.0206	0.3087	0.0141	0.4849	-9.9957	31.986	-19.1125
15	0.0112	0.0313	-0.0137	0.1448	-0.0055	0.0253	0.0957	-0.1324	-0.2096	-0.2215	-0.0353	0.0077	-0.3352	0.4154	-0.0004	0.5848	-0.0484	-0.1518	0.3835	0.0666	0.354	-4.3432	35.1787	-22.7498
16	0.4442	0.016	0.6886	1.209	-0.8142	1.7081	0.2349	-0.3939	0.0494	0.5004	0.1697	-0.1308	-0.7327	0.1252	0.6404	0.3467	-0.0727	-0.0262	0.3102	-0.097	0.2404	-0.4692	26.087	-2.203

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:20)
2	X-RAY DIFFRACTION	2	(chain A and resid 21:38)
3	X-RAY DIFFRACTION	3	(chain A and resid 39:56)
4	X-RAY DIFFRACTION	4	(chain A and resid 57:83)
5	X-RAY DIFFRACTION	5	(chain A and resid 84:97)
6	X-RAY DIFFRACTION	6	(chain A and resid 98:137)
7	X-RAY DIFFRACTION	7	(chain A and resid 138:152)
8	X-RAY DIFFRACTION	8	(chain A and resid 153:205)
9	X-RAY DIFFRACTION	9	(chain A and resid 206:217)
10	X-RAY DIFFRACTION	10	(chain A and resid 218:229)
11	X-RAY DIFFRACTION	11	(chain A and resid 230:247)
12	X-RAY DIFFRACTION	12	(chain A and resid 248:272)
13	X-RAY DIFFRACTION	13	(chain B and resid 1:8)
14	X-RAY DIFFRACTION	14	(chain B and resid 9:14)
15	X-RAY DIFFRACTION	15	(chain C and resid 15:20)
16	X-RAY DIFFRACTION	16	(chain C and resid 21:28)

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