PDB-3umv: Eukaryotic Class II CPD photolyase structure reveals a basis for ...

ID or keywords:

Entry

Database: PDB / ID: 3umv

Title

Eukaryotic Class II CPD photolyase structure reveals a basis for improved UV-tolerance in plants

Components

Deoxyribodipyrimidine photo-lyase

Photolyase

Keywords

LYASE / CPD cyclobutane pyrimidine dimers / UV damaged DNA /

DNA repair /

flavoprotein

Function / homology

Function and homology information

photoreactive repair /

deoxyribodipyrimidine photo-lyase /

deoxyribodipyrimidine photo-lyase activity /

UV protection / FAD binding /

DNA repair /

DNA binding /

nucleus
Similarity search - Function

Biological species

Oryza sativa Japonica Group (Japanese rice)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.705 Å

Authors

Arvai, A.S. / Hitomi, K. / Getzoff, E.D. / Tainer, J.A.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Eukaryotic Class II Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals Basis for Improved Ultraviolet Tolerance in Plants.
Authors: Hitomi, K. / Arvai, A.S. / Yamamoto, J. / Hitomi, C. / Teranishi, M. / Hirouchi, T. / Yamamoto, K. / Iwai, S. / Tainer, J.A. / Hidema, J. / Getzoff, E.D.

History

Deposition	Nov 14, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 21, 2011	Provider: repository / Type: Initial release
Revision 1.1	May 2, 2012	Group: Database references
Revision 1.2	Sep 13, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3umv.cif.gz	422.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3umv.ent.gz	342.4 KB	Display	PDB format
PDBx/mmJSON format	3umv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/um/3umv ftp://data.pdbj.org/pub/pdb/validation_reports/um/3umv	HTTPS FTP

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Related structure data

Related structure data	1dnpS 1iqrS 1qnfS S: Starting model for refinement
Similar structure data	5c5h-1 4xwr-d 3e34-3 3b6d-d 1aq6-d 4gxq-3 2j4d-2 6lr8-d 3l8c-1 1qq5-d 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	#91 - Jul 2007 Thymine Dimers similarity (6)

Deposited unit

A: Deoxyribodipyrimidine photo-lyase

B: Deoxyribodipyrimidine photo-lyase

hetero molecules

116 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Deoxyribodipyrimidine photo-lyase

hetero molecules

defined by author&software
58.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Deoxyribodipyrimidine photo-lyase

hetero molecules

defined by author&software
57.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.351, 109.362, 97.742
Angle α, β, γ (deg.)	90.00, 93.59, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Deoxyribodipyrimidine photo-lyase / Photolyase / DNA photolyase / OsCPDII / Photoreactivating enzyme Mass: 56691.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: PHR, Os10g0167600, LOC_Os10g08580, OSJNAb0015J03.12 / Plasmid: pGEX_OsPHR_sasanishiki / Production host: Escherichia coli (E. coli) References: UniProt: Q6F6A2, deoxyribodipyrimidine photo-lyase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#4: Chemical	ChemComp-URE / UREA / Urea Mass: 60.055 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH₄N₂O
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1289 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	AUTHORS STATE THAT THE CORRECT SEQUENCE HAS A GLN AT POSITION 126. THE CORRECT SEQUENCE HAS BEEN ...AUTHORS STATE THAT THE CORRECT SEQUENCE HAS A GLN AT POSITION 126. THE CORRECT SEQUENCE HAS BEEN DEPOSITED TO THE GENBANK.

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 50.99 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 35% PEG 4K, 5% saturated Urea, 200 mM immidazole malate , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.979764 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2004
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979764 Å / Relative weight: 1
Reflection	Resolution: 1.7→50 Å / Num. all: 119326 / Num. obs: 119326 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / R_merge(I) obs: 0.056 / R_sym value: 0.056 / Net I/σ(I): 23.1
Reflection shell	Resolution: 1.7→1.76 Å / R_merge(I) obs: 0.341 / Mean I/σ(I) obs: 2.87 / R_sym value: 0.341 / % possible all: 98

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
AMoRE		phasing
PHENIX	(phenix.refine: 1.6.1_357)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 1DNP, 1QNF, and 1IQR

1dnp

1qnf

1iqr

Resolution: 1.705→45.555 Å / SU ML: 0.21 / σ(F): 0.03 / Phase error: 21.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2166	1784	1.69 %	random
R_work	0.181	-	-	-
obs	0.1816	105749	86.9 %	-
all	-	119326	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 47.917 Å² / k_sol: 0.322 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.2594 Å²	-0 Å²	-3.9218 Å²
2-	-	-4.7982 Å²	-0 Å²
3-	-	-	-2.4613 Å²

Refinement step

Cycle: LAST / Resolution: 1.705→45.555 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7448	0	166	1289	8903

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7903
X-RAY DIFFRACTION	f_angle_d	1.052	10736
X-RAY DIFFRACTION	f_dihedral_angle_d	15.67	2910
X-RAY DIFFRACTION	f_chiral_restr	0.071	1108
X-RAY DIFFRACTION	f_plane_restr	0.005	1392

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 (%)
1.705-1.7511	0.2353	124	0.1798	7235	X-RAY DIFFRACTION	79
1.7511-1.8026	0.2245	137	0.1739	7955	X-RAY DIFFRACTION	87
1.8026-1.8608	0.2104	131	0.1868	7449	X-RAY DIFFRACTION	81
1.8608-1.9273	0.4526	103	0.3751	5949	X-RAY DIFFRACTION	65
1.9273-2.0045	0.2189	105	0.2186	6346	X-RAY DIFFRACTION	69
2.0045-2.0957	0.2559	147	0.185	8616	X-RAY DIFFRACTION	94
2.0957-2.2062	0.2222	144	0.1924	8112	X-RAY DIFFRACTION	88
2.2062-2.3444	0.3333	115	0.2904	7065	X-RAY DIFFRACTION	77
2.3444-2.5254	0.1977	157	0.1698	8909	X-RAY DIFFRACTION	97
2.5254-2.7795	0.1992	154	0.1679	8974	X-RAY DIFFRACTION	98
2.7795-3.1816	0.2219	155	0.1668	9056	X-RAY DIFFRACTION	98
3.1816-4.0081	0.1753	153	0.1419	9040	X-RAY DIFFRACTION	98
4.0081-45.5708	0.1552	159	0.1321	9259	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	0.7295	0.0373	-0.4558	0.052	0.0108	1.4532	0.0399	-0.067	0.2915	0.0632	0.1216	-0.1058	-0.1778	0.1677	-0.1791	0.1634	-0.0182	0.0031	0.1665	-0.0086	0.3163	13.7168	23.8083	12.9369
2	1.1943	-0.5859	-0.1618	0.3919	0.2605	0.4496	-0.0341	0.0356	0.2081	0.0002	-0.0508	0.1666	-0.1261	-0.134	0.0138	0.0828	0.0472	0.0067	0.1194	-0.0033	0.2078	2.3715	20.6269	12.2747
3	0.6186	0.0232	-0.1527	0.2036	-0.1475	0.1537	0.0026	0.0244	-0.0243	0.0033	0.0513	0.25	-0.0665	-0.0706	-0.0327	0.0526	0.0215	0.0229	0.2091	-0.0159	0.2601	-3.4577	5.1154	10.2672
4	0.118	0.0495	0.0665	0.823	0.1451	0.5151	0.0166	0.0529	0.157	-0.0518	0.0664	-0.0684	-0.116	0.0284	-0.1019	0.0752	0.0199	0.001	0.1297	0.0006	0.1834	12.7791	16.8079	7.611
5	0.3092	0.1423	-0.0636	0.1214	-0.1102	0.1163	-0.0305	0.0882	0.1027	0.0639	0.0531	0.3807	-0.1031	-0.2697	0.2126	-0.1701	0.0803	-0.0234	0.1804	-0.0573	0.3452	-8.7784	10.7903	11.0912
6	0.8708	-0.1004	-0.3682	2.1123	0.7891	0.4281	-0.0836	-0.101	-0.0563	0.6037	0.076	0.1516	0.246	-0.0509	0.0054	0.2115	0.0244	0.0353	0.1054	0.0009	0.0955	10.3986	-3.7509	23.4166
7	0.6173	-0.1845	0.1271	2.568	1.1204	0.5834	-0.0392	0.0374	-0.0134	0.757	0.1262	-0.1925	0.2213	0.1076	-0.0314	0.3205	0.0411	-0.0641	0.162	-0.0427	0.1542	20.8535	4.6697	29.4846
8	0.4554	-0.0577	-0.4015	0.5598	-0.0068	0.3778	-0.0768	0.0345	-0.0098	-0.0399	0.0354	-0.0091	0.0441	-0.0109	0.0316	0.0481	-0.0078	0.017	0.1101	-0.0143	0.1121	21.9984	-9.349	4.1187
9	1.7834	0.054	0.016	0.4388	0.5339	0.8222	-0.1215	0.0165	0.0451	0.3046	0.1023	0.1353	0.433	0.0246	0.0113	0.2796	-0.024	0.0683	0.1655	0.0749	0.2445	12.7689	-21.9699	17.8103
10	0.0387	0.0517	0.0124	0.059	0.0192	0.0064	-0.0597	0.0303	-0.0216	0.0377	0.0247	0.0094	-0.0075	-0.065	0	0.096	-0.0062	0.0029	0.1593	0.0005	0.124	14.0907	-1.9143	11.1859
11	0.4029	0.1511	-0.0796	1.1506	0.5194	0.644	0.0336	-0.0914	-0.0179	0.2741	-0.1424	0.0962	-0.1273	-0.1458	0.0915	0.5099	-0.0146	-0.0237	0.1296	-0.0132	0.1014	19.958	74.3279	56.0142
12	0.4809	-0.1203	0.2388	0.4101	0.309	0.7879	-0.0905	-0.0671	0.0344	-0.1031	-0.0485	-0.0169	-0.5405	-0.069	0.0801	0.5607	0.013	-0.0322	0.1489	0.007	0.1269	23.466	80.4427	39.7113
13	0.3921	0.1185	-0.2328	0.4522	0.5216	1.4638	0.0268	-0.0439	-0.0169	0.3499	-0.112	-0.0119	0.282	-0.1011	0.0875	0.5084	-0.0438	-0.0284	0.1286	-0.0068	0.1127	23.4293	65.0031	52.5601
14	0.4306	-0.108	-0.134	0.7808	1.4369	2.7131	-0.0362	0.079	0.2124	-0.3781	-0.1155	0.0482	-0.8678	0.1162	0.1531	0.792	-0.0278	-0.0595	0.1478	0.0422	0.1836	23.2049	86.555	43.1395
15	0.3957	-0.0488	-0.1526	0.5979	0.2687	1.8965	-0.1047	0.1394	0.0363	-0.233	-0.3029	0.1255	-0.3037	-0.7869	0.2255	0.2498	0.0748	-0.0334	0.4264	-0.1969	0.1669	5.7158	66.2636	30.371
16	0.7981	-0.1558	-0.1025	0.5429	0.1576	0.3369	0.0208	0.0928	-0.023	0.1143	-0.308	0.1054	0.2226	-0.44	0.2099	0.3585	-0.0921	0.0661	0.3391	-0.133	0.1579	6.8452	61.0997	39.9767
17	0.2367	-0.6385	-0.3478	1.7005	0.9652	0.5866	-0.0186	0.012	0.0297	0.5174	-0.0255	-0.1925	0.3202	-0.0029	0.0679	0.3641	0.0298	-0.0666	0.1398	0.0205	0.1299	31.1421	49.1885	34.7967
18	0.0873	-0.0186	-0.1412	0.5462	0.3811	1.0962	-0.0104	-0.0277	0.0066	0.2296	-0.0541	-0.01	0.121	-0.091	0.0559	0.2635	-0.0051	-0.0068	0.1208	0.0019	0.0869	24.9834	54.488	23.7802
19	0.2282	-0.4125	-0.2354	1.922	0.3106	1.5397	0.0069	0.1689	0.0462	0.1239	-0.3404	0.1106	-0.183	-0.5369	0.2781	0.2662	0.0216	-0.0355	0.3053	-0.0651	0.1932	11.9284	59.1417	14.2981
20	0.0013	-0.0039	0.0034	0.0086	-0.0201	0.0462	0.0644	-0.0693	0.0276	0.0431	-0.1255	0.0533	0.0928	-0.0566	0.0001	0.3139	-0.0073	0.0103	0.1923	-0.0291	0.1516	17.2668	61.0146	33.5594

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 19:29)
2	X-RAY DIFFRACTION	2	(chain A and resid 30:76)
3	X-RAY DIFFRACTION	3	(chain A and resid 77:118)
4	X-RAY DIFFRACTION	4	(chain A and resid 119:204)
5	X-RAY DIFFRACTION	5	(chain A and resid 205:234)
6	X-RAY DIFFRACTION	6	(chain A and resid 235:296)
7	X-RAY DIFFRACTION	7	(chain A and resid 297:318)
8	X-RAY DIFFRACTION	8	(chain A and resid 319:465)
9	X-RAY DIFFRACTION	9	(chain A and resid 466:490)
10	X-RAY DIFFRACTION	10	(chain A and resid 701:999)
11	X-RAY DIFFRACTION	11	(chain B and resid 19:76)
12	X-RAY DIFFRACTION	12	(chain B and resid 77:121)
13	X-RAY DIFFRACTION	13	(chain B and resid 122:205)
14	X-RAY DIFFRACTION	14	(chain B and resid 206:235)
15	X-RAY DIFFRACTION	15	(chain B and resid 236:279)
16	X-RAY DIFFRACTION	16	(chain B and resid 280:323)
17	X-RAY DIFFRACTION	17	(chain B and resid 324:361)
18	X-RAY DIFFRACTION	18	(chain B and resid 362:466)
19	X-RAY DIFFRACTION	19	(chain B and resid 467:486)
20	X-RAY DIFFRACTION	20	(chain B and resid 701:999)

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