PDB-4frg: Crystal structure of the cobalamin riboswitch aptamer domain

ID or keywords:

Entry

Database: PDB / ID: 4frg

Title

Crystal structure of the cobalamin riboswitch aptamer domain

Components

cobalamin riboswitch aptamer domain

Keywords

RNA /

cobalamin /

riboswitch / B12

Function / homology

Hydroxocobalamin / IRIDIUM (III) ION /

RNA / RNA (> 10)

Function and homology information

Biological species

Marine metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.95 Å

Authors

Reyes, F.E. / Johnson, J.E. / Polaski, J.T. / Batey, R.T.

Citation

Journal: Nature / Year: 2012
Title: B12 cofactors directly stabilize an mRNA regulatory switch.
Authors: Johnson, J.E. / Reyes, F.E. / Polaski, J.T. / Batey, R.T.

History

Deposition	Jun 26, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 17, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 26, 2012	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	4frg.cif.gz	196.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4frg.ent.gz	160.5 KB	Display	PDB format
PDBx/mmJSON format	4frg.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/fr/4frg ftp://data.pdbj.org/pub/pdb/validation_reports/fr/4frg	HTTPS FTP

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Related structure data

Related structure data	4frnC 4gmaC C: citing same article (ref.)
Similar structure data	6q3m-4 5nui-d 1jia-d 6guu-2 4dge-2 4xrn-2 3jsy-1 5xoc-d 1y2g-d 3hct-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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (2) #15 - Mar 2001 Transfer RNA similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #10 - Oct 2000 Ribosome similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #161 - May 2013 Ricin similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #227 - Nov 2018 Telomerase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (2)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (2)
#15 - Mar 2001
Transfer RNA
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

B: cobalamin riboswitch aptamer domain

X: cobalamin riboswitch aptamer domain

hetero molecules

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

1

B: cobalamin riboswitch aptamer domain

hetero molecules

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

2

X: cobalamin riboswitch aptamer domain

hetero molecules

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

Unit cell

Length a, b, c (Å)	142.030, 142.030, 137.900
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	181
Space group name H-M	P6₄22

#1: RNA chain	cobalamin riboswitch aptamer domain Mass: 27135.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA was transcribed via in vitro T7 RNA polymerase / Source: (synth.) Marine metagenome (others)
#2: Chemical	ChemComp-I2A / Hydroxocobalamin / Hydroxocobalamin Mass: 1345.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆₂H₈₈CoN₁₃O₁₅P
#3: Chemical	ChemComp-IR3 / IRIDIUM (III) ION / Iridium Mass: 192.217 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Ir
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
Sequence details	THE SEQUENCE CAN BE FOUND AT GENBANK ACCESSION #: AACY021350931.1/557-477 OBTAINED FROM SHOTGUN ...THE SEQUENCE CAN BE FOUND AT GENBANK ACCESSION #: AACY021350931.1/557-477 OBTAINED FROM SHOTGUN SEQUENCING. THERE ARE SIX SUBSTITUTIONS TO THE ORIGINAL SEQUENCE TO FACILITATE CRYSTALLIZATION: UACUUG TO CGAAAG(THIS REGION OCCURS RESIDUE NUMBER 46 TO 51 IN THE PDB)

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Experiment

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

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	3.7	66.5
2	3.7	66.5

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
298	1	hanging drop	7	100 mM magnesium acetate, 10% 2-methyl-1,3-propanediol, 5 mM iridium hexammine, pH 7.0, hanging drop, temperature 298K
298	2	hanging drop	7	100 mM magnesium acetate, 10% 2-methyl-1,3-propanediol, 5 mM iridium hexammine, pH 7.0, hanging drop, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		2

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ALS	5.0.2	1	1.1051, 1.6
	ALS	5.0.2	2

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2010

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.1051	1
2	1.6	1

Reflection

Redundancy: 13.5 % / Av σ(I) over netI: 6.8 / Number: 192234 / R_sym value: 0.082 / D res high: 3.16 Å / D res low: 137.897 Å / Num. obs: 14220 / % possible obs: 97.2

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
9.99	137.9	97.1	1	0.037	0.037	10.7
7.07	9.99	100	1	0.042	0.042	12.1
5.77	7.07	100	1	0.048	0.048	12.6
5	5.77	100	1	0.054	0.054	13.2
4.47	5	100	1	0.077	0.077	13.7
4.08	4.47	100	1	0.099	0.099	13.9
3.78	4.08	88.7	1	0.144	0.144	13.7
3.53	3.78	89.7	1	0.239	0.239	13.8
3.33	3.53	100	1	0.301	0.301	14.1
3.16	3.33	100	1	0.485	0.485	14.2

Reflection

Resolution: 2.95→137.899 Å / Num. all: 17854 / Num. obs: 17854 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / R_sym value: 0.098 / Net I/σ(I): 20.6

Reflection shell

R_merge(I) obs: 0.014 / Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.95-3.11	14.2	0.5	36032	2536	1.406	100
3.11-3.3	14.2	1.3	34413	2425	0.573	100
3.3-3.53	14.1	2.4	32191	2277	0.313	100
3.53-3.81	14.1	3.2	29927	2125	0.231	100
3.81-4.17	14	5.5	27512	1966	0.134	100
4.17-4.66	13.8	8.3	24734	1789	0.09	100
4.66-5.39	13.5	11.1	21624	1605	0.064	100
5.39-6.6	12.8	12.8	17818	1388	0.051	100
6.6-9.33	12.2	13.4	13339	1092	0.043	100
9.33-137.899	10.9	14.3	7109	651	0.038	97.7

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 3.16 Å / D res low: 43.06 Å / FOM acentric: 0.358 / FOM centric: 0.227 / Reflection acentric: 11936 / Reflection centric: 2423

Phasing MAD set

Highest resolution: 3.16 Å / Lowest resolution: 43.06 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	7881	1848
ISO_2	0.78	0.831	0.865	0.755	7881	1841
ANO_1	0.789	0	0.837	0	7881	0
ANO_2	0.8	0	1.128	0	11936	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	13.46-43.06	0	0	0	0	68	87
ISO_1	9.76-13.46	0	0	0	0	188	115
ISO_1	8.04-9.76	0	0	0	0	283	125
ISO_1	6.99-8.04	0	0	0	0	353	127
ISO_1	6.27-6.99	0	0	0	0	408	113
ISO_1	5.73-6.27	0	0	0	0	457	122
ISO_1	5.32-5.73	0	0	0	0	505	113
ISO_1	4.98-5.32	0	0	0	0	549	125
ISO_1	4.7-4.98	0	0	0	0	577	126
ISO_1	4.46-4.7	0	0	0	0	626	116
ISO_1	4.25-4.46	0	0	0	0	657	130
ISO_1	4.07-4.25	0	0	0	0	695	129
ISO_1	3.91-4.07	0	0	0	0	709	126
ISO_1	3.77-3.91	0	0	0	0	762	122
ISO_1	3.65-3.77	0	0	0	0	779	126
ISO_1	3.53-3.65	0	0	0	0	265	46
ISO_1	3.43-3.53	0	0	0	0	0	0
ISO_1	3.33-3.43	0	0	0	0	0	0
ISO_1	3.24-3.33	0	0	0	0	0	0
ISO_1	3.16-3.24	0	0	0	0	0	0
ANO_1	13.46-43.06	0.576	0	1.374	0	68	0
ANO_1	9.76-13.46	0.592	0	1.219	0	188	0
ANO_1	8.04-9.76	0.608	0	1.392	0	283	0
ANO_1	6.99-8.04	0.624	0	1.355	0	353	0
ANO_1	6.27-6.99	0.615	0	1.409	0	408	0
ANO_1	5.73-6.27	0.692	0	1.13	0	457	0
ANO_1	5.32-5.73	0.723	0	1.064	0	505	0
ANO_1	4.98-5.32	0.771	0	0.933	0	549	0
ANO_1	4.7-4.98	0.822	0	0.807	0	577	0
ANO_1	4.46-4.7	0.884	0	0.615	0	626	0
ANO_1	4.25-4.46	0.921	0	0.512	0	657	0
ANO_1	4.07-4.25	0.949	0	0.45	0	695	0
ANO_1	3.91-4.07	0.96	0	0.393	0	709	0
ANO_1	3.77-3.91	0.975	0	0.326	0	762	0
ANO_1	3.65-3.77	0.98	0	0.269	0	779	0
ANO_1	3.53-3.65	0.991	0	0.234	0	265	0
ANO_1	3.43-3.53	0	0	0	0	0	0
ANO_1	3.33-3.43	0	0	0	0	0	0
ANO_1	3.24-3.33	0	0	0	0	0	0
ANO_1	3.16-3.24	0	0	0	0	0	0
ISO_2	13.46-43.06	0.754	0.85	1.305	1.015	68	86
ISO_2	9.76-13.46	0.858	0.832	1.247	1.087	188	114
ISO_2	8.04-9.76	0.885	0.976	1.291	0.895	283	125
ISO_2	6.99-8.04	0.866	1.022	1.076	0.811	353	125
ISO_2	6.27-6.99	0.848	0.903	1.069	0.684	408	113
ISO_2	5.73-6.27	0.873	0.901	0.842	0.652	457	122
ISO_2	5.32-5.73	0.875	0.866	0.74	0.575	505	113
ISO_2	4.98-5.32	0.864	0.9	0.719	0.444	549	122
ISO_2	4.7-4.98	0.879	0.881	0.652	0.51	577	126
ISO_2	4.46-4.7	0.831	0.818	0.571	0.43	626	116
ISO_2	4.25-4.46	0.831	0.854	0.509	0.392	657	130
ISO_2	4.07-4.25	0.832	0.855	0.506	0.353	695	129
ISO_2	3.91-4.07	0.789	0.754	0.446	0.374	709	126
ISO_2	3.77-3.91	0.809	0.814	0.427	0.277	762	122
ISO_2	3.65-3.77	0.739	0.768	0.377	0.261	779	126
ISO_2	3.53-3.65	0.71	0.846	0.347	0.255	265	46
ISO_2	3.43-3.53	0	0	0	0	0	0
ISO_2	3.33-3.43	0	0	0	0	0	0
ISO_2	3.24-3.33	0	0	0	0	0	0
ISO_2	3.16-3.24	0	0	0	0	0	0
ANO_2	13.46-43.06	0.456	0	2.73	0	68	0
ANO_2	9.76-13.46	0.464	0	2.714	0	188	0
ANO_2	8.04-9.76	0.491	0	2.857	0	283	0
ANO_2	6.99-8.04	0.482	0	2.79	0	353	0
ANO_2	6.27-6.99	0.498	0	2.668	0	408	0
ANO_2	5.73-6.27	0.554	0	2.129	0	457	0
ANO_2	5.32-5.73	0.595	0	1.965	0	505	0
ANO_2	4.98-5.32	0.667	0	1.643	0	549	0
ANO_2	4.7-4.98	0.727	0	1.37	0	577	0
ANO_2	4.46-4.7	0.764	0	1.164	0	626	0
ANO_2	4.25-4.46	0.829	0	0.98	0	657	0
ANO_2	4.07-4.25	0.869	0	0.898	0	695	0
ANO_2	3.91-4.07	0.902	0	0.841	0	709	0
ANO_2	3.77-3.91	0.934	0	0.653	0	762	0
ANO_2	3.65-3.77	0.941	0	0.508	0	779	0
ANO_2	3.53-3.65	0.966	0	0.468	0	804	0
ANO_2	3.43-3.53	0.978	0	0.389	0	846	0
ANO_2	3.33-3.43	0.983	0	0.322	0	867	0
ANO_2	3.24-3.33	0.99	0	0.309	0	884	0
ANO_2	3.16-3.24	0.993	0	0.265	0	919	0

Phasing MAD shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
13.46-43.06	0.767	0.513	68	87
9.76-13.46	0.756	0.466	188	115
8.04-9.76	0.759	0.376	283	125
6.99-8.04	0.707	0.337	353	128
6.27-6.99	0.714	0.357	408	113
5.73-6.27	0.669	0.333	457	122
5.32-5.73	0.609	0.323	505	113
4.98-5.32	0.572	0.268	549	126
4.7-4.98	0.523	0.239	577	126
4.46-4.7	0.49	0.256	626	116
4.25-4.46	0.427	0.219	657	130
4.07-4.25	0.376	0.168	695	129
3.91-4.07	0.332	0.19	709	126
3.77-3.91	0.288	0.149	762	122
3.65-3.77	0.263	0.152	779	126
3.53-3.65	0.195	0.092	804	125
3.43-3.53	0.162	0.077	846	121
3.33-3.43	0.131	0.054	867	128
3.24-3.33	0.114	0.053	884	117
3.16-3.24	0.087	0.035	919	128

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
SHARP		phasing
SOLOMON		phasing
BUSTER-TNT		refinement
PDB_EXTRACT	3.11	data extraction
BOS		data collection
XDS		data reduction
BUSTER	2.10.0	refinement

Refinement

Method to determine structure:

MAD / Resolution: 2.95→43.06 Å / Cor.coef. F_o:F_c: 0.9009 / Cor.coef. F_o:F_c free: 0.9198 / Occupancy max: 1 / Occupancy min: 0.85 / SU R Cruickshank DPI: 0.84 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2491	910	5.11 %	RANDOM
R_work	0.2393	-	-	-
all	0.2397	18377	-	-
obs	0.2397	17822	99.92 %	-

Displacement parameters

B_iso max: 300 Å² / B_iso mean: 103.2693 Å² / B_iso min: 56.07 Å²

Refine analyze

Luzzati coordinate error obs: 0.784 Å

Refinement step

Cycle: LAST / Resolution: 2.95→43.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	3600	217	0	3817

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	978	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes
X-RAY DIFFRACTION	t_gen_planes	190	HARMONIC	5
X-RAY DIFFRACTION	t_it	4238	HARMONIC	20
X-RAY DIFFRACTION	t_nbd	0	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	672	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle	2	HARMONIC	1
X-RAY DIFFRACTION	t_utility_torsion	1680	SINUSOIDAL	1
X-RAY DIFFRACTION	t_ideal_dist_contact	3845	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	4238	HARMONIC	2	0.008
X-RAY DIFFRACTION	t_angle_deg	6636	HARMONIC	2	0.64
X-RAY DIFFRACTION	t_omega_torsion
X-RAY DIFFRACTION	t_other_torsion				21.89

LS refinement shell

Resolution: 2.95→3.13 Å / Total num. of bins used: 9

	R_factor	Num. reflection	% reflection
R_free	0.2928	153	5.44 %
R_work	0.2527	2662	-
all	0.2549	2815	-
obs	-	-	99.92 %

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	2.0319	1.9	-0.5923	3.6924	-1.3251	3.1161	-0.1339	0.0976	-0.3779	-0.1489	0.0783	-0.3643	-0.0525	0.1901	0.0556	-0.1175	-0.1679	-0.184	-0.0472	-0.0008	0.0518	18.2198	-55.2862	23.2251
2	1.3269	-0.0927	1.2008	2.6	-1.1837	5.7037	0.0469	-0.0643	-0.045	0.096	0.0471	0.1781	0.2062	-0.5372	-0.0941	0.0086	0.1418	0.1147	-0.0049	-0.1676	-0.177	37.3555	-23.8169	-14.9109

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	1 - 84
2	X-RAY DIFFRACTION	2	X	1 - 84

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