PDB-4c2t: Crystal structure of full length Deinococcus radiodurans UvrD in ...

ID or keywords:

Entry

Database: PDB / ID: 4c2t

Title

Crystal structure of full length Deinococcus radiodurans UvrD in complex with DNA

Components

DNA HELICASE IIHelicase
DNA STRAND FOR28
DNA STRAND REV28

Keywords

HYDROLASE/DNA / HYDROLASE-DNA COMPLEX /

DNA REPAIR /

DNA HELICASES /

NUCLEOTIDE EXCISION REPAIR

Function / homology

Function and homology information

DNA helicase complex / DNA 3'-5' helicase /

recombinational repair / 3'-5' DNA helicase activity /

ATP hydrolysis activity /

DNA binding /

ATP binding /

cytosol
Similarity search - Function

Biological species

DEINOCOCCUS RADIODURANS (radioresistant)
SYNTHETIC CONSTRUCT (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.997 Å

Authors

Stelter, M. / Acajjaoui, S. / McSweeney, S. / Timmins, J.

Citation

Journal: Plos One / Year: 2013
Title: Structural and Mechanistic Insight Into DNA Unwinding by Deinococcus Radiodurans Uvrd.
Authors: Stelter, M. / Acajjaoui, S. / Mcsweeney, S. / Timmins, J.

History

Deposition	Aug 20, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 30, 2013	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4c2t.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb4c2t.ent.gz	940 KB	Display	PDB format
PDBx/mmJSON format	4c2t.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/c2/4c2t ftp://data.pdbj.org/pub/pdb/validation_reports/c2/4c2t	HTTPS FTP

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Related structure data

Related structure data	4c2uC 4c30C C: citing same article (ref.)
Similar structure data	4c2u-d 4md9-2 5epm-d 4md7-1 7ky9-d 4md8-2 6z3u-d 4wa6-3 3rko-1 1qiu-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	#168 - Dec 2013 DNA Helicase similarity (11) #67 - Jul 2005 TATA-Binding Protein similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (9) #91 - Jul 2007 Thymine Dimers similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #253 - Jan 2021 Expressome similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #135 - Mar 2011 Integrase similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #73 - Jan 2006 Topoisomerase similarity (2) #40 - Apr 2003 RNA Polymerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #23 - Nov 2001 DNA similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #131 - Nov 2010 Inteins similarity (1) #125 - May 2010 Parvoviruses similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #108 - Dec 2008 Hsp90 similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#168 - Dec 2013
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TATA-Binding Protein
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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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similarity (1)
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similarity (1)
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similarity (1)
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similarity (1)
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Parvoviruses
similarity (1)
#119 - Nov 2009
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similarity (1)
#241 - Jan 2020
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similarity (1)
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similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
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similarity (1)
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similarity (1)
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Deposited unit

A: DNA HELICASE II

B: DNA HELICASE II

C: DNA HELICASE II

D: DNA HELICASE II

M: DNA STRAND FOR28

N: DNA STRAND REV28

O: DNA STRAND REV28

P: DNA STRAND FOR28

hetero molecules

367 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DNA HELICASE II

B: DNA HELICASE II

M: DNA STRAND FOR28

N: DNA STRAND REV28

hetero molecules

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

2

C: DNA HELICASE II

D: DNA HELICASE II

O: DNA STRAND REV28

P: DNA STRAND FOR28

hetero molecules

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

Unit cell

Length a, b, c (Å)	71.457, 390.044, 71.559
Angle α, β, γ (deg.)	90.00, 106.13, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	DNA HELICASE II / Helicase / UVRD Mass: 82707.492 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RTI9, DNA helicase
#2: DNA chain	DNA STRAND FOR28 Mass: 8569.497 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain	DNA STRAND REV28 Mass: 8578.511 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 57.91 % / Description: NONE
Crystal grow	Details: 16-22% PEG 3350, 0.1 M BIS-TRIS PROPANE PH 6.5-7.5, 0.1-0.3 M NA-NITRATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9395
Detector	Type: ADSC QUANTUM 315r / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9395 Å / Relative weight: 1
Reflection	Resolution: 4→46.1 Å / Num. obs: 30051 / % possible obs: 99.6 % / Redundancy: 4.4 % / B_iso Wilson estimate: 149.79 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 10.1
Reflection shell	Resolution: 4→4.22 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.66 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: DIFFERENT CRYSTAL FORM OF DRUVRD

Resolution: 3.997→46.147 Å / SU ML: 0.53 / σ(F): 0 / Phase error: 30.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2713	1516	5 %
R_work	0.2464	-	-
obs	0.2477	30051	94.51 %

Solvent computation

Shrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 167.099 Å² / k_sol: 0.361 e/Å³

Displacement parameters

B_iso mean: 207.7 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	12.0222 Å²	0 Å²	23.0968 Å²
2-	-	-32.4405 Å²	0 Å²
3-	-	-	20.4183 Å²

Refinement step

Cycle: LAST / Resolution: 3.997→46.147 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20337	2080	128	0	22545

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	23161
X-RAY DIFFRACTION	f_angle_d	1.075	31771
X-RAY DIFFRACTION	f_dihedral_angle_d	18.905	8786
X-RAY DIFFRACTION	f_chiral_restr	0.079	3507
X-RAY DIFFRACTION	f_plane_restr	0.005	3824

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 (%)
3.9971-4.126	0.4142	129	0.406	2183	X-RAY DIFFRACTION	80
4.126-4.2734	0.4309	120	0.3621	2368	X-RAY DIFFRACTION	86
4.2734-4.4444	0.3598	137	0.3106	2513	X-RAY DIFFRACTION	92
4.4444-4.6465	0.322	123	0.2828	2554	X-RAY DIFFRACTION	94
4.6465-4.8912	0.2956	138	0.2703	2657	X-RAY DIFFRACTION	96
4.8912-5.1972	0.2524	155	0.2507	2685	X-RAY DIFFRACTION	97
5.1972-5.5979	0.3132	140	0.27	2658	X-RAY DIFFRACTION	98
5.5979-6.1601	0.3575	155	0.2898	2697	X-RAY DIFFRACTION	99
6.1601-7.0487	0.3054	143	0.2633	2750	X-RAY DIFFRACTION	99
7.0487-8.8703	0.1971	144	0.2032	2750	X-RAY DIFFRACTION	100
8.8703-46.1505	0.1924	132	0.1817	2720	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	4.584	2.0173	-0.7854	1.1259	-2.7031	4.6335	0.1774	1.5638	-0.6118	-0.8991	-0.2018	0.6788	0.456	-0.745	-0	2.2335	0.129	0.1242	1.7976	-0.2257	1.9337	-52.5174	-103.2967	-8.4292
2	5.138	-1.8204	1.7132	2.9589	-2.2703	3.9541	0.758	-0.1073	-0.62	0.1591	-0.3308	-1.0617	0.1222	0.4334	0	2.1425	-0.407	-0.0531	1.9126	0.2035	1.8287	-21.8042	-111.9825	3.5837
3	3.2369	2.5952	-2.3488	6.3045	-1.9329	1.2959	0.4232	-0.3551	0.4007	0.2953	-0.2877	0.1981	-0.3574	-0.0366	0	1.8754	-0.1174	-0.1427	1.7914	-0.1058	1.3239	-50.1672	-107.9924	5.6969
4	1.0707	0.7955	0.8152	2.5278	0.8448	3.0596	-0.284	0.4971	-1.1676	-0.8719	0.3202	0.152	0.0989	0.5626	-0	1.9499	-0.0208	-0.0296	1.8598	0.0523	1.6334	-51.084	-132.6799	2.1255
5	0.8352	-1.3332	0.822	0.8807	-0.6024	1.6002	0.1703	-0.3978	0.5303	0.1534	-0.3274	-1.3008	0.387	0.1532	0	2.346	0.139	-0.0057	2.3091	-0.1817	2.2988	-18.8226	-126.0395	-12.9791
6	2.728	1.3213	0.4179	2.4561	1.1732	1.2406	-0.42	1.2477	-1.065	-0.3409	0.2295	0.4046	-0.0761	0.1914	0	3.0984	0.1143	0.0994	2.6878	-0.3947	2.044	-31.1526	-128.2686	-19.9352
7	6.6067	0.7597	0.7266	6.3747	-1.2552	1.5246	0.1152	-0.7644	-0.3269	0.6986	-0.1995	-0.2833	0.0708	0.3012	0	1.6377	-0.2068	0.0029	1.8684	0.1096	1.1144	-51.7355	-124.9539	15.5171
8	3.1555	-0.532	0.5415	2.0425	1.1022	4.5113	-0.0497	0.6408	-0.363	-0.8218	-0.4338	0.7336	-0.9289	-1.3039	-0	1.8113	0.1174	0.1098	1.7155	0.0269	2.2609	5.9362	-181.0939	-48.0217
9	1.6549	-0.4143	-0.3731	2.8476	0.559	6.0584	0.5003	0.0715	-0.2138	0.7704	-0.652	-0.1038	0.0208	-0.063	-0	1.6904	-0.1117	-0.1171	1.6937	0.1564	2.1571	9.7061	-178.3495	-21.8466
10	0.0509	0.8023	-0.7622	4.9734	-0.2481	2.1206	-0.3199	0.055	-0.9724	-0.192	-0.2288	-0.2883	0.7849	0.2376	0	1.6582	0.0903	-0.1334	1.8579	0.063	1.9608	18.7595	-185.2543	-46.4351
11	3.6987	-0.1497	1.0882	3.9623	0.0334	0.9132	0.312	-0.185	0.3465	-0.6409	0.196	0.3257	-0.8802	-0.0973	0	1.6628	-0.0863	-0.0756	1.678	0.1877	1.7561	22.9086	-153.7694	-51.5357
12	1.0708	-2.5381	2.7369	0.0402	0.21	1.8279	0.1064	-0.7029	-0.269	0.6173	-0.2137	0.555	0.2611	0.0974	-0	2.0727	0.063	0.0021	2.4983	0.1643	2.59	-8.2634	-161.6817	-21.483
13	0.6141	-1.1675	-0.3245	2.3036	-1.7085	4.4624	-0.1852	0.3933	0.453	-0.4744	0.3119	-0.2296	-0.4854	-1.4341	-0	1.9456	0.3598	-0.3737	2.9022	-0.1524	2.7895	-10.7621	-158.6886	-35.8961
14	3.0027	2.0561	-0.9004	8.1788	-1.968	4.3343	-0.2095	0.1818	-0.1711	0.5634	-0.0969	-1.1223	-0.551	0.3704	0	1.1628	-0.0382	-0.1649	1.8801	0.1491	1.4989	29.2814	-161.9491	-45.4532
15	3.8178	-1.0013	-0.5426	4.255	0.7716	4.3109	-0.0865	-2.115	1.3501	1.1551	-0.4672	1.2076	-0.1138	-0.9338	0	2.2559	-0.3227	0.0767	2.2739	-0.2561	1.8635	-17.2106	-87.7527	32.6687
16	4.9196	1.0918	0.176	1.6392	-0.2046	1.3238	0.6076	-0.2286	1.2203	0.1576	-0.2599	-0.6018	-0.3159	0.6647	0	2.035	0.0943	0.2028	2.0066	0.0199	2.3406	13.7807	-79.1112	20.4329
17	4.3346	-0.3078	1.0088	3.6386	-0.9916	2.1736	0.3106	-0.1225	0.3136	-0.2979	-0.3211	0.1723	0.1187	-0.0814	0	2.0071	-0.1873	-0.008	1.8857	-0.0712	1.6984	-14.6394	-83.6099	18.0942
18	0.4869	0.3846	-0.3084	0.4718	-0.6653	2.3272	0.1112	-0.832	0.8286	1.2225	-0.3494	0.3516	-0.9005	0.154	-0	2.717	-0.221	0.1928	1.9922	-0.3642	3.1445	-16.3021	-58.9454	20.5083
19	0.8544	1.7083	0.511	0.1574	0.2217	0.0251	0.2679	-0.2642	-0.6944	0.3394	-0.203	-0.5133	-0.0302	0.3788	0	2.72	-0.4922	0.0422	2.705	-0.4689	2.6553	16.5849	-65.1626	37.1011
20	2.3741	1.7615	-4.3658	1.8993	-1.5703	-0.1567	0.2147	-0.4478	0.5241	1.4551	-0.6263	0.2859	-0.25	0.1452	-0	3.6253	-0.2278	-0.0819	2.611	-0.4243	2.6013	6.0895	-62.5711	43.5881
21	3.828	-0.1716	0.9988	3.1569	-1.9792	2.4801	0.0801	0.4383	0.9744	-0.2478	-0.0956	0.925	-0.6236	-0.1275	-0	2.3846	0.0358	-0.0372	1.9141	0.029	2.4042	-16.3654	-66.8332	8.8785
22	2.8734	1.5423	0.5715	2.8099	2.1508	1.3376	-0.4834	-0.0652	0.2888	0.392	-0.5171	1.0591	1.4252	-1.5322	0	2.0084	-0.0185	-0.0877	2.2373	-0.3236	2.3601	17.9177	-6.6036	71.2232
23	1.5039	-0.3673	-1.3134	1.6396	1.6633	4.513	-0.3667	0.6479	-0.5874	-0.5812	0.0308	-0.5829	0.4165	0.0191	0	2.053	-0.0758	0.2868	1.9253	0.0779	2.13	37.5398	-10.6553	50.484
24	1.8829	-0.962	0.7381	4.2305	0.0364	4.152	-0.0703	0.0492	-0.0974	0.6799	-0.5169	0.1224	0.4533	-0.0799	-0	1.8734	0.1023	-0.0845	1.9569	-0.0242	2.1039	29.992	-8.3562	77.5994
25	2.9261	-1.2145	1.8237	1.3853	-0.247	0.3445	0.3795	0.4294	-0.7711	0.1698	-0.1946	1	1.3423	-0.7849	-0	2.7551	-0.2167	0.0562	2.0262	-0.3684	2.7723	27.1854	-33.0412	78.4814
26	-0.0325	-0.0334	0.1637	-0.0543	1.3609	0.3509	0.2186	-0.181	-0.066	-1.219	0.0886	-1.3781	-0.1437	0.543	0	2.8065	-0.2818	0.1611	2.7644	-0.3531	2.7073	21.0154	-27.5082	42.692
27	1.1848	-3.3113	-1.5768	2.5862	0.9323	1.9401	0.0406	0.2962	0.0819	-0.0272	-0.6238	1.3067	0.3133	-0.6815	-0	2.4487	-0.4478	-0.1035	2.9188	-0.4344	3.047	11.8095	-29.374	50.5563
28	2.3458	-0.2032	0.7657	3.9553	0.3683	4.6187	-0.7082	-0.7935	-0.84	0.665	0.2509	-0.0836	1.1357	0.0565	0	2.469	0.1409	-0.0919	1.9242	0.1081	2.2443	39.4992	-24.8118	82.2335

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 7:113)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 114:194)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 195:348)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 349:391)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 392:440)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 454:555)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 562:662)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 7:132)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 133:208)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 209:317)
11	X-RAY DIFFRACTION	11	(CHAIN B AND RESID 318:388)
12	X-RAY DIFFRACTION	12	(CHAIN B AND RESID 389:453)
13	X-RAY DIFFRACTION	13	(CHAIN B AND RESID 454:552)
14	X-RAY DIFFRACTION	14	(CHAIN B AND RESID 562:662)
15	X-RAY DIFFRACTION	15	(CHAIN C AND RESID 7:113)
16	X-RAY DIFFRACTION	16	(CHAIN C AND RESID 114:194)
17	X-RAY DIFFRACTION	17	(CHAIN C AND RESID 195:348)
18	X-RAY DIFFRACTION	18	(CHAIN C AND RESID 349:391)
19	X-RAY DIFFRACTION	19	(CHAIN C AND RESID 392:442)
20	X-RAY DIFFRACTION	20	(CHAIN C AND RESID 443:551)
21	X-RAY DIFFRACTION	21	(CHAIN C AND RESID 552:662)
22	X-RAY DIFFRACTION	22	(CHAIN D AND RESID 7:133)
23	X-RAY DIFFRACTION	23	(CHAIN D AND RESID 134:194)
24	X-RAY DIFFRACTION	24	(CHAIN D AND RESID 195:348)
25	X-RAY DIFFRACTION	25	(CHAIN D AND RESID 349:391)
26	X-RAY DIFFRACTION	26	(CHAIN D AND RESID 392:440)
27	X-RAY DIFFRACTION	27	(CHAIN D AND RESID 441:555)
28	X-RAY DIFFRACTION	28	(CHAIN D AND RESID 562:661)

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