PDB-4c30: Crystal structure of Deinococcus radiodurans UvrD in complex with...

ID or keywords:

Entry

Database: PDB / ID: 4c30

Title

Crystal structure of Deinococcus radiodurans UvrD in complex with DNA, form 2

Components

DNA HELICASE IIHelicase
DNA STRAND FOR25
DNA STRAND REV25

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 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 21, 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	4c30.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb4c30.ent.gz	947 KB	Display	PDB format
PDBx/mmJSON format	4c30.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/c3/4c30 ftp://data.pdbj.org/pub/pdb/validation_reports/c3/4c30	HTTPS FTP

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Related structure data

Related structure data	4c2tC 4c2uC C: citing same article (ref.)
Similar structure data	4c2t-2 4fw8-d 5lbs-2 3pqb-d 11838 5jhh-d 3q6i-d 5lbs-1 7caf-d 6z3u-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

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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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similarity (1)
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similarity (1)
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similarity (1)
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Parvoviruses
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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Deposited unit

A: DNA HELICASE II

D: DNA HELICASE II

F: DNA HELICASE II

I: DNA HELICASE II

K: DNA STRAND FOR25

L: DNA STRAND REV25

X: DNA STRAND FOR25

Y: DNA STRAND REV25

hetero molecules

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

1

A: DNA HELICASE II

D: DNA HELICASE II

X: DNA STRAND FOR25

Y: DNA STRAND REV25

hetero molecules

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

2

F: DNA HELICASE II

I: DNA HELICASE II

K: DNA STRAND FOR25

L: DNA STRAND REV25

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.489, 89.785, 293.798
Angle α, β, γ (deg.)	90.00, 89.97, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(1, -0.00111, -0.001577), (-0.001109, -1, 0.000448), (-0.001577, -0.000447, -1)	34.45, 45.44, 146.9
2	given	(1, 0.000293, 0.00019), (0.000293, -1, 0.000567), (0.00019, -0.5667, -1)	34.2, 45.52, 146.9
3	given	(1, -0.000233, -0.001388), (-0.000233, -1, -0.000208), (-0.001388, 0.000208, -1)	34.42, 45.58, 146.9
4	given	(1, -0.00172, -0.002548), (-0.00172, -1, -4.5E-5), (-0.002548, 5.0E-5, -1)	34.55, 45.54, 146.9

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Protein , 1 types, 4 molecules ADFI

#1: Protein	DNA HELICASE II / Helicase / UVRD Mass: 74100.484 Da / Num. of mol.: 4 / Fragment: C-TERMINAL TRUNCATION, RESIDUES 1-665 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Plasmid: PET151D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RTI9, DNA helicase

#1: Protein

DNA HELICASE II /

Helicase / UVRD

Mass: 74100.484 Da / Num. of mol.: 4 / Fragment: C-TERMINAL TRUNCATION, RESIDUES 1-665
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

DEINOCOCCUS RADIODURANS (radioresistant)
Plasmid: PET151D / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RTI9,

DNA helicase

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DNA chain , 2 types, 4 molecules KXLY

#2: DNA chain	DNA STRAND FOR25 Mass: 7677.927 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain	DNA STRAND REV25 Mass: 7615.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 105 molecules

#4: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.75 Å³/Da / Density % sol: 60.02 % / Description: NONE
Crystal grow	Details: 22% PEG 3350, 0.1 M BIS-TRIS PROPANE PH 7.5, 0.1 M NA-FLUORIDE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.078
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.078 Å / Relative weight: 1
Reflection	Resolution: 3→66.2 Å / Num. obs: 62649 / % possible obs: 89 % / Redundancy: 1.5 % / B_iso Wilson estimate: 72.3 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 6.5
Reflection shell	Resolution: 3→3.16 Å / Redundancy: 1.4 % / R_merge(I) obs: 0.32 / Mean I/σ(I) obs: 1.9 / % possible all: 86.5

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0085	refinement
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: DRUVRD FORM1

Resolution: 3→66.18 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.889 / SU B: 57.527 / SU ML: 0.486 / Cross valid method: THROUGHOUT / ESU R Free: 0.56 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28783	3128	5 %	RANDOM
R_work	0.2282	-	-	-
obs	0.23114	59507	87.23 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 104.631 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.5 Å²	0 Å²	-0.01 Å²
2-	-	-0.6 Å²	0 Å²
3-	-	-	-6.91 Å²

Refinement step

Cycle: LAST / Resolution: 3→66.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20008	1876	68	97	22049

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	22463
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.544	2.059	30547
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.292	5	2530
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.336	23.369	1042
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.029	15	3475
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.164	15	219
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	3408
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	16688
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3→3.078 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.365	241	-
R_work	0.337	4153	-
obs	-	-	83.84 %

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	0.6531	-0.0009	0.0635	0.4632	-1.0451	4.3406	-0.0448	-0.0355	-0.095	-0.0605	-0.0247	-0.2095	0.6916	-0.5273	0.0695	1.1556	-0.3	-0.0378	0.8701	-0.0079	0.3754	7.063	-7.095	-26.458
2	0.9906	0.2201	0.11	1.4003	-0.0455	1.8614	0.0912	-0.1136	0.0847	-0.0311	-0.1865	0.0457	0.1373	0.0149	0.0953	0.7343	0.0028	0.0205	0.8669	0.089	0.5986	27.767	12.681	-32.114
3	0.666	-0.1035	-0.2954	0.1452	-0.2966	2.1707	-0.1876	-0.0129	-0.0859	0.0917	0.0213	-0.1898	0.0142	-0.5187	0.1663	1.013	0.0301	-0.0915	0.9578	0.0692	0.4854	14.404	9.23	-13.045
4	0.5407	-0.3813	-0.0127	0.9957	0.0862	0.7763	0.0838	0.0989	-0.1224	0.1973	-0.1579	0.0964	0.1074	0.0239	0.074	0.7187	0.0029	0.0446	0.7969	-0.0354	0.6375	20.112	-0.526	62.092
5	1.8455	0.2468	0.0037	1.7696	0.5744	1.4196	-0.044	-0.0154	0.1127	0.0078	-0.2211	-0.167	-0.3957	0.0019	0.2651	0.8217	0.0753	-0.0644	0.8337	0.0196	0.6059	35.593	2.415	35.544
6	1.2319	0.1789	1.4849	2.9742	-1.1778	3.1026	0.1684	0.0947	0.0936	0.2503	-0.1159	0.3899	0.0811	0.0824	-0.0525	0.5964	0.0751	0.0639	0.8504	-0.1034	0.7228	6.162	16.678	62.604
7	0.6537	0.1029	0.2752	0.3754	-0.7874	4.6739	-0.1186	0.0225	0.0535	-0.0337	-0.0199	-0.2301	-0.5615	-0.6465	0.1385	1.1759	0.358	0.0702	0.9113	-0.0132	0.3868	-28.52	51.499	171.089
8	1.2277	-0.7399	-0.0173	0.9215	-0.1067	1.6349	0.0539	0.1153	-0.0682	0.0952	-0.1678	-0.1306	-0.4813	-0.0185	0.1139	0.9097	0.0132	0.025	0.7993	0.0735	0.5467	-12.52	41.632	179.943
9	0.4276	0.1538	0.0803	0.1687	-0.2512	1.7753	-0.2099	0.0172	-0.0358	-0.0943	0.0822	-0.2143	-0.188	-0.5079	0.1277	0.9934	0.0081	0.1073	1.0212	0.0535	0.4914	-19.896	36.329	160.041
10	0.612	0.4744	0.1329	1.0248	0.1923	0.6556	0.1038	-0.0701	0.1256	-0.1425	-0.1625	0.1016	-0.0723	0.0121	0.0587	0.7588	0.0208	0.0104	0.7974	-0.0325	0.6276	-14.17	46.135	84.886
11	1.3089	0.0244	0.2699	1.6673	0.3343	1.485	-0.0214	-0.0084	-0.0958	-0.1274	-0.1772	-0.2188	0.3969	-0.0789	0.1986	0.878	-0.0681	0.1136	0.8418	0.0233	0.5854	1.634	43.339	111.687
12	2.1147	0.0603	-1.2374	2.0062	-0.9681	3.4051	0.0182	-0.217	0.0776	-0.1407	0.0129	0.1855	0.0662	0.1743	-0.0311	0.5974	-0.0552	0.0149	0.8334	-0.0895	0.6893	-28.101	28.906	84.389
13	0.0627	-0.0849	0.288	2.5069	0.544	6.2999	-0.0914	0.1711	0.0098	0.1343	-0.3917	-0.1461	0.1734	-0.4438	0.4831	1.01	-0.2379	-0.0644	1.0525	0.1204	0.2923	-15.59	34.737	127.252
14	21.2533	-12.0781	-7.2272	6.9092	4.4861	5.6883	0.0601	2.5762	-0.0325	-0.1933	-1.3644	0.1874	-1.4224	0.1038	1.3043	1.1051	-0.034	-0.275	1.1175	0.4492	0.8205	-10.584	43.954	163.052
15	2.5459	-2.0602	-1.4035	12.4423	2.362	0.9951	0.0118	0.0856	0.6306	1.2204	0.7745	-0.0215	0.0065	-0.2745	-0.7863	1.5204	-0.0652	-0.2383	2.0054	0.5879	0.8083	-7.703	36.779	145.346
16	3.5863	0.2119	1.7729	0.555	-0.8744	2.6733	-0.2598	-0.6632	0.0173	-0.0602	0.1877	-0.0817	0.0722	-0.8454	0.0721	1.2483	-0.262	-0.0063	0.8235	-0.1394	0.4007	-21.358	35.989	111.912
17	0.0659	0.1853	0.3502	0.6803	1.1683	4.3604	-0.0988	-0.1816	-0.0394	-0.1139	-0.3084	-0.2029	-0.0528	-0.1862	0.4072	0.9867	0.2562	0.0646	1.0064	0.1584	0.3072	18.702	10.847	19.739
18	36.9486	14.8536	17.0949	5.9875	6.5616	15.864	-0.2934	-1.2297	0.0519	-0.0632	-0.6461	-0.0088	0.4816	0.6759	0.9395	1.0585	-0.0582	0.1143	0.837	0.224	0.3922	23.717	1.632	-15.993
19	3.6356	-2.3502	3.2804	5.6467	1.0224	5.4318	0.0721	-1.6085	-0.1051	-0.4751	0.6407	-0.3165	0.0121	-1.7037	-0.7128	1.3587	0.2444	0.2106	1.384	0.2705	0.5931	26.541	8.845	1.612
20	3.0364	-0.0963	-1.3335	0.6246	-0.8879	2.1832	-0.2033	0.5753	0.1091	-0.0762	0.0613	-0.0085	0.0229	-0.7271	0.142	1.0827	0.2959	-0.046	0.8226	-0.1405	0.4053	12.937	9.603	35.079

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 286
2	X-RAY DIFFRACTION	2	A	287 - 392
3	X-RAY DIFFRACTION	3	A	393 - 661
4	X-RAY DIFFRACTION	4	D	7 - 384
5	X-RAY DIFFRACTION	5	D	385 - 550
6	X-RAY DIFFRACTION	6	D	559 - 662
7	X-RAY DIFFRACTION	7	F	7 - 226
8	X-RAY DIFFRACTION	8	F	227 - 392
9	X-RAY DIFFRACTION	9	F	393 - 661
10	X-RAY DIFFRACTION	10	I	7 - 384
11	X-RAY DIFFRACTION	11	I	385 - 550
12	X-RAY DIFFRACTION	12	I	559 - 662
13	X-RAY DIFFRACTION	13	K	1 - 17
14	X-RAY DIFFRACTION	14	K	18 - 23
15	X-RAY DIFFRACTION	15	L	1 - 7
16	X-RAY DIFFRACTION	16	L	8 - 23
17	X-RAY DIFFRACTION	17	X	1 - 17
18	X-RAY DIFFRACTION	18	X	18 - 23
19	X-RAY DIFFRACTION	19	Y	1 - 7
20	X-RAY DIFFRACTION	20	Y	8 - 23

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