PDB-2vtb: Structure of cryptochrome 3 - DNA complex

ID or keywords:

Entry

Database: PDB / ID: 2vtb

Title

Structure of cryptochrome 3 - DNA complex

Components

(CRYPTOCHROME ...) x 2
5'-D(*DT*DT*DT*DT*DTP)-3'

Keywords

LYASE/DNA / LYASE-DNA COMPLEX / LYASE DNA COMPLEX / FLAVIN ADENINE DINUCLEOTIDE / DNA / DNA-BINDING / CRYPTOCHROME / FLAVOPROTEIN / MITOCHONDRION / FAD / PHOTOLYASE / CHROMOPHORE / CHLOROPLAST / TRANSIT PEPTIDE / SINGLE-STRANDED DNA / CYCLOBUTANE-PYRIMIDINE DIMER

Function / homology

Function and homology information

DNA photolyase activity / photoreactive repair / photoreceptor activity / chloroplast / mitochondrion / DNA binding / ATP binding
Similarity search - Function

Biological species

ARABIDOPSIS THALIANA (thale cress)

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.01 Å

Authors

Pokorny, R. / Klar, T. / Hennecke, U. / Carell, T. / Batschauer, A. / Essen, L.-O.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Recognition and Repair of Uv Lesions in Loop Structures of Duplex DNA by Dash-Type Cryptochrome.
Authors: Pokorny, R. / Klar, T. / Hennecke, U. / Carell, T. / Batschauer, A. / Essen, L.-O.

History

Deposition	May 13, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 2, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jul 24, 2019	Group: Advisory / Data collection / Derived calculations Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms ...diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3	Dec 13, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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	2vtb.cif.gz	646.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2vtb.ent.gz	527.7 KB	Display	PDB format
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Validation report

Summary document	2vtb_validation.pdf.gz	3.9 MB	Display	wwPDB validaton report
Full document	2vtb_full_validation.pdf.gz	3.9 MB	Display
Data in XML	2vtb_validation.xml.gz	118.9 KB	Display
Data in CIF	2vtb_validation.cif.gz	165.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vt/2vtb ftp://data.pdbj.org/pub/pdb/validation_reports/vt/2vtb	HTTPS FTP

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Related structure data

Related structure data	2j4dS S: Starting model for refinement
Similar structure data	2j4d-d 6mi8-d 5xbs-d 6pc1-1 4yro-1 3giq-d 6mhz-d 6x99-2 3ihv-d 4h2f-1 Search similar-shape structures by Omokage search (details) 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

Related structure data

2j4dS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#23 - Nov 2001 DNA similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (8)

Deposited unit

A: CRYPTOCHROME DASH

B: CRYPTOCHROME DASH

C: CRYPTOCHROME DASH

D: CRYPTOCHROME DASH

E: CRYPTOCHROME DASH

F: CRYPTOCHROME DASH

G: 5'-D(*DT*DT*DT*DT*DTP)-3'

H: 5'-D(*DT*DT*DT*DT*DTP)-3'

I: 5'-D(*DT*DT*DT*DT*DTP)-3'

J: 5'-D(*DT*DT*DT*DT*DTP)-3'

K: 5'-D(*DT*DT*DT*DT*DTP)-3'

L: 5'-D(*DT*DT*DT*DT*DTP)-3'

hetero molecules

379 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CRYPTOCHROME DASH

B: CRYPTOCHROME DASH

G: 5'-D(*DT*DT*DT*DT*DTP)-3'

H: 5'-D(*DT*DT*DT*DT*DTP)-3'

hetero molecules

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

2

C: CRYPTOCHROME DASH

D: CRYPTOCHROME DASH

I: 5'-D(*DT*DT*DT*DT*DTP)-3'

J: 5'-D(*DT*DT*DT*DT*DTP)-3'

hetero molecules

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

3

E: CRYPTOCHROME DASH

F: CRYPTOCHROME DASH

K: 5'-D(*DT*DT*DT*DT*DTP)-3'

L: 5'-D(*DT*DT*DT*DT*DTP)-3'

hetero molecules

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

Unit cell

Length a, b, c (Å)	120.734, 136.082, 211.484
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ILE	ILE	VAL	VAL	5	A	A	4 - 352	5 - 353
2	1	ILE	ILE	VAL	VAL	5	B	B	4 - 352	5 - 353
3	1	ILE	ILE	VAL	VAL	5	C	C	4 - 352	5 - 353
4	1	ILE	ILE	VAL	VAL	5	D	D	4 - 352	5 - 353
5	1	ILE	ILE	VAL	VAL	5	E	E	4 - 352	5 - 353
6	1	ILE	ILE	VAL	VAL	5	F	F	4 - 352	5 - 353
1	2	FAD	FAD	MHF	MHF	4	A	M - N	998 - 999
2	2	FAD	FAD	MHF	MHF	4	B	P - Q	998 - 999
3	2	FAD	FAD	MHF	MHF	4	C	U - V	998 - 999
4	2	FAD	FAD	MHF	MHF	4	D	Y - Z	998 - 999
5	2	FAD	FAD	MHF	MHF	4	E	BA - CA	998 - 999
6	2	FAD	FAD	MHF	MHF	4	F	EA - FA	998 - 999
1	3	TRP	TRP	GLY	GLY	5	A	A	356 - 437	357 - 438
2	3	TRP	TRP	GLY	GLY	5	B	B	356 - 437	357 - 438
3	3	TRP	TRP	GLY	GLY	5	C	C	356 - 437	357 - 438
4	3	TRP	TRP	GLY	GLY	5	D	D	356 - 437	357 - 438
5	3	TRP	TRP	GLY	GLY	5	E	E	356 - 437	357 - 438
6	3	TRP	TRP	GLY	GLY	5	F	F	356 - 437	357 - 438
1	4	SER	SER	LEU	LEU	5	A	A	449 - 474	450 - 475
2	4	SER	SER	LEU	LEU	5	B	B	449 - 474	449 - 474
3	4	SER	SER	LEU	LEU	5	C	C	449 - 474	450 - 475
4	4	SER	SER	LEU	LEU	5	D	D	449 - 474	450 - 475
5	4	SER	SER	LEU	LEU	5	E	E	449 - 474	450 - 475
6	4	SER	SER	LEU	LEU	5	F	F	449 - 474	450 - 475
1	5	MET	MET	LEU	LEU	5	A	A	486 - 494	487 - 495
2	5	MET	MET	LEU	LEU	5	B	B	486 - 494	486 - 494
3	5	MET	MET	LEU	LEU	5	C	C	486 - 494	487 - 495
4	5	MET	MET	LEU	LEU	5	D	D	486 - 494	487 - 495
5	5	MET	MET	LEU	LEU	5	E	E	486 - 494	487 - 495
6	5	MET	MET	LEU	LEU	5	F	F	486 - 494	487 - 495

NCS ensembles :

ID
1
2
3
4
5

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.32031, 0.88836, -0.32897), (0.88228, -0.4062, -0.23786), (-0.34493, -0.21405, -0.91389)	-72.1289, 68.98244, -101.61922
2	given	(0.36483, 0.85893, -0.35937), (0.85551, -0.46156, -0.23466), (-0.36742, -0.22183, -0.90321)	-95.8792, 54.41899, -232.42484
3	given	(0.42141, 0.86868, 0.26038), (0.87339, -0.46606, 0.14133), (0.24413, 0.16786, -0.95511)	38.15336, -17.56623, -154.36839

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CRYPTOCHROME ... , 2 types, 6 molecules ACDEFB

#1: Protein	CRYPTOCHROME DASH / CRYPTOCHROME 3 Mass: 60463.809 Da / Num. of mol.: 5 / Fragment: CRYPTOCHROME DASH, RESIDUES 44-569 Source method: isolated from a genetically manipulated source Details: MATURE PROTEIN WITHOUT PLASTID IMPORT SEQUENCE / Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PQE-60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15-PREP4 References: UniProt: Q84KJ5, deoxyribodipyrimidine photo-lyase
#2: Protein	CRYPTOCHROME DASH / CRYPTOCHROME 3 Mass: 60392.730 Da / Num. of mol.: 1 Fragment: CRYPTOCHROME DASH, RESIDUES 44-482,484-489,490-569 Source method: isolated from a genetically manipulated source Details: MATURE PROTEIN WITHOUT PLASTID IMPORT SEQUENCE / Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PQE-60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15-PREP4 References: UniProt: Q84KJ5, deoxyribodipyrimidine photo-lyase

#1: Protein

CRYPTOCHROME DASH / CRYPTOCHROME 3

Mass: 60463.809 Da / Num. of mol.: 5 / Fragment: CRYPTOCHROME DASH, RESIDUES 44-569
Source method: isolated from a genetically manipulated source
Details: MATURE PROTEIN WITHOUT PLASTID IMPORT SEQUENCE / Source: (gene. exp.)

ARABIDOPSIS THALIANA (thale cress) / Plasmid: PQE-60 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): M15-PREP4
References: UniProt: Q84KJ5, deoxyribodipyrimidine photo-lyase

#2: Protein

CRYPTOCHROME DASH / CRYPTOCHROME 3

Mass: 60392.730 Da / Num. of mol.: 1
Fragment: CRYPTOCHROME DASH, RESIDUES 44-482,484-489,490-569
Source method: isolated from a genetically manipulated source
Details: MATURE PROTEIN WITHOUT PLASTID IMPORT SEQUENCE / Source: (gene. exp.)

ARABIDOPSIS THALIANA (thale cress) / Plasmid: PQE-60 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): M15-PREP4
References: UniProt: Q84KJ5, deoxyribodipyrimidine photo-lyase

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DNA chain , 1 types, 6 molecules GHIJKL

#3: DNA chain	5'-D(DTDTDTDTDTP)-3' / T5-OLIGONUCLEOTIDE Mass: 1410.054 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: FORMACETAL LINKAGE REPLACES PHOSPHATE / Source: (synth.) HOMO SAPIENS* (human)

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Non-polymers , 5 types, 1326 molecules

#4: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#5: Chemical	ChemComp-MHF / 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID Mass: 457.440 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₀H₂₃N₇O₆
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1305 / Source method: isolated from a natural source / Formula: H₂O

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Details

Nonpolymer details	FLAVIN-ADENINE DINUCLEOTIDE (FAD): CATALYTIC COFACTOR 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID (MHF): ...FLAVIN-ADENINE DINUCLEOTIDE (FAD): CATALYTIC COFACTOR 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID (MHF): ANTENNA CHROMOPHORE
Sequence details	ACCORDING TO THE AUTHOR CHAIN B DIFFERS IN THE SEQUENCE FOR THIS ENTRY DUE TO A LOCAL FRAMESHIFT ...ACCORDING TO THE AUTHOR CHAIN B DIFFERS IN THE SEQUENCE FOR THIS ENTRY DUE TO A LOCAL FRAMESHIFT DURING THE SEQUENCE ASSIGNMENT.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.4 % / Description: NONE
Crystal grow	pH: 4.6 Details: 10 MG/ML PROTEIN, 85 MM NA-CITRATE PH 4.6, 170 MM NH4-ACETATE, 21.5% (W/V) PEG 4000 AND 15% (V/V) GLYCEROL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8125
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jan 26, 2007 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8125 Å / Relative weight: 1
Reflection	Resolution: 2→15.1 Å / Num. obs: 229217 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.02 % / R_merge(I) obs: 0.1 / Net I/σ(I): 14.9
Reflection shell	Resolution: 2→2.05 Å / R_merge(I) obs: 0.41 / Mean I/σ(I) obs: 2.8 / % possible all: 89.6

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J4D

2j4d

Resolution: 2.01→15.03 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.931 / SU B: 7.462 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SYNTHETIC CPD LESION AT POSITION 2 & 3 REPAIRED BY SYNCHROTRON RADIATION

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.222	1518	0.7 %	RANDOM
R_work	0.184	-	-	-
obs	0.185	227588	99.2 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 35.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.08 Å²	0 Å²	0 Å²
2-	-	-0.02 Å²	0 Å²
3-	-	-	0.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.01→15.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23956	520	528	1305	26309

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	25705
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	17839
X-RAY DIFFRACTION	r_angle_refined_deg	1.151	2.003	34960
X-RAY DIFFRACTION	r_angle_other_deg	0.867	3	42999
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.451	5	2936
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.206	22.869	1192
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.852	15	4188
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.282	15	212
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	3632
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	27894
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5560
X-RAY DIFFRACTION	r_nbd_refined	0.197	0.2	5122
X-RAY DIFFRACTION	r_nbd_other	0.183	0.2	18191
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	12484
X-RAY DIFFRACTION	r_nbtor_other	0.079	0.2	11977
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.131	0.2	1321
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	0.246	0.2	47
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.217	0.2	131
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.171	0.2	39
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	0.471	1.5	15155
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.8	2	23679
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.014	3	12853
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.622	4.5	11277
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

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	2009	medium positional	0.14	0.5
1	2	B	2009	medium positional	0.19	0.5
1	3	C	2009	medium positional	0.2	0.5
1	4	D	2009	medium positional	0.21	0.5
1	5	E	2009	medium positional	0.28	0.5
1	6	F	2009	medium positional	0.16	0.5
2	1	A	125	medium positional	0.07	0.5
2	2	B	125	medium positional	0.06	0.5
2	3	C	125	medium positional	0.1	0.5
2	4	D	125	medium positional	0.06	0.5
2	5	E	125	medium positional	0.06	0.5
2	6	F	125	medium positional	0.06	0.5
3	1	A	482	medium positional	0.09	0.5
3	2	B	482	medium positional	0.08	0.5
3	3	C	482	medium positional	0.08	0.5
3	4	D	482	medium positional	0.07	0.5
3	5	E	482	medium positional	0.08	0.5
3	6	F	482	medium positional	0.09	0.5
4	1	A	153	medium positional	0.14	0.5
4	2	B	153	medium positional	0.14	0.5
4	3	C	153	medium positional	0.11	0.5
4	4	D	153	medium positional	0.13	0.5
4	5	E	153	medium positional	0.11	0.5
4	6	F	153	medium positional	0.15	0.5
5	1	A	53	medium positional	0.15	0.5
5	2	B	53	medium positional	0.1	0.5
5	3	C	53	medium positional	0.09	0.5
5	4	D	53	medium positional	0.16	0.5
5	5	E	53	medium positional	0.13	0.5
5	6	F	53	medium positional	0.17	0.5
1	1	A	2723	loose positional	0.44	5
1	2	B	2723	loose positional	0.33	5
1	3	C	2723	loose positional	0.45	5
1	4	D	2723	loose positional	0.43	5
1	5	E	2723	loose positional	0.6	5
1	6	F	2723	loose positional	0.34	5
3	1	A	657	loose positional	0.3	5
3	2	B	657	loose positional	0.24	5
3	3	C	657	loose positional	0.46	5
3	4	D	657	loose positional	0.29	5
3	5	E	657	loose positional	0.44	5
3	6	F	657	loose positional	0.49	5
4	1	A	233	loose positional	0.71	5
4	2	B	233	loose positional	0.64	5
4	3	C	233	loose positional	0.41	5
4	4	D	233	loose positional	0.56	5
4	5	E	233	loose positional	0.5	5
4	6	F	233	loose positional	0.55	5
5	1	A	64	loose positional	0.47	5
5	2	B	64	loose positional	0.41	5
5	3	C	64	loose positional	0.55	5
5	4	D	64	loose positional	0.43	5
5	5	E	64	loose positional	0.4	5
5	6	F	64	loose positional	0.56	5
1	1	A	2009	medium thermal	0.35	2
1	2	B	2009	medium thermal	0.32	2
1	3	C	2009	medium thermal	0.47	2
1	4	D	2009	medium thermal	0.4	2
1	5	E	2009	medium thermal	0.35	2
1	6	F	2009	medium thermal	0.33	2
2	1	A	125	medium thermal	0.28	2
2	2	B	125	medium thermal	0.3	2
2	3	C	125	medium thermal	0.4	2
2	4	D	125	medium thermal	0.31	2
2	5	E	125	medium thermal	0.35	2
2	6	F	125	medium thermal	0.34	2
3	1	A	482	medium thermal	0.27	2
3	2	B	482	medium thermal	0.22	2
3	3	C	482	medium thermal	0.29	2
3	4	D	482	medium thermal	0.25	2
3	5	E	482	medium thermal	0.3	2
3	6	F	482	medium thermal	0.21	2
4	1	A	153	medium thermal	0.64	2
4	2	B	153	medium thermal	0.24	2
4	3	C	153	medium thermal	0.24	2
4	4	D	153	medium thermal	0.38	2
4	5	E	153	medium thermal	0.37	2
4	6	F	153	medium thermal	0.24	2
5	1	A	53	medium thermal	0.48	2
5	2	B	53	medium thermal	0.7	2
5	3	C	53	medium thermal	0.81	2
5	4	D	53	medium thermal	0.39	2
5	5	E	53	medium thermal	0.2	2
5	6	F	53	medium thermal	0.38	2
1	1	A	2723	loose thermal	0.87	10
1	2	B	2723	loose thermal	0.72	10
1	3	C	2723	loose thermal	0.89	10
1	4	D	2723	loose thermal	0.8	10
1	5	E	2723	loose thermal	0.86	10
1	6	F	2723	loose thermal	0.9	10
3	1	A	657	loose thermal	0.57	10
3	2	B	657	loose thermal	0.51	10
3	3	C	657	loose thermal	0.69	10
3	4	D	657	loose thermal	0.44	10
3	5	E	657	loose thermal	0.67	10
3	6	F	657	loose thermal	0.67	10
4	1	A	233	loose thermal	1.06	10
4	2	B	233	loose thermal	0.57	10
4	3	C	233	loose thermal	0.87	10
4	4	D	233	loose thermal	0.63	10
4	5	E	233	loose thermal	0.87	10
4	6	F	233	loose thermal	0.89	10
5	1	A	64	loose thermal	0.98	10
5	2	B	64	loose thermal	0.84	10
5	3	C	64	loose thermal	1.16	10
5	4	D	64	loose thermal	0.86	10
5	5	E	64	loose thermal	0.63	10
5	6	F	64	loose thermal	0.65	10

LS refinement shell

Resolution: 2.01→2.06 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.314	69
R_work	0.223	14867

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	0.4885	0.0911	-0.1948	0.2205	0.1684	0.5093	-0.029	-0.0158	0.0229	-0.0251	0.0198	0.0107	0.0064	0.0978	0.0091	-0.0483	0.0162	0.0399	-0.0637	0.0159	-0.0838	-28.5859	16.146	-60.1751
2	0.5568	-0.1502	-0.1001	0.8299	-0.1022	0.7454	-0.0062	-0.1088	0.1787	0.0833	0.0682	0.0107	-0.1427	0.0742	-0.062	-0.0218	0.0089	0.0718	-0.0484	-0.0306	0.0323	-47.2074	51.1779	-39.4121
3	0.5865	-0.2032	0.2915	0.3166	-0.1421	0.7604	0.0559	-0.0057	-0.0401	-0.1183	0.017	0.1198	0.095	-0.0148	-0.0729	-0.0843	-0.0245	-0.0338	-0.0812	0.0155	-0.0482	-29.5329	15.7099	-128.2576
4	0.6208	-0.3798	0.0262	0.7815	-0.181	0.8046	-0.1022	-0.0753	0.1545	0.0927	0.0283	-0.1823	-0.1727	0.1113	0.0739	-0.064	0.0179	-0.0368	-0.0288	-0.0215	-0.0237	-47.395	51.1641	-108.7082
5	0.6189	0.1261	-0.1809	0.3102	-0.0102	0.6145	0.048	0.1034	-0.0075	0.025	-0.0238	0.0441	-0.0019	-0.1067	-0.0242	-0.0599	0.0161	0.0263	-0.0568	0.0122	-0.0869	-32.5823	-15.9538	-93.9466
6	1.0795	-0.4759	-0.283	2.2325	-0.6485	1.3033	0.0287	-0.1694	-0.2938	0.2445	-0.2118	0.0238	0.039	0.1978	0.1831	-0.0057	-0.0149	-0.0176	0.0312	0.0842	0.0117	-13.0599	-51.0669	-75.7587
7	8.8707	1.928	-3.3055	0.501	-0.159	5.0507	0.1057	-0.2514	0.2591	-0.1004	-0.0302	0.2338	-0.3432	0.2342	-0.0755	-0.001	-0.0013	0.0167	0.0052	0.0186	-0.0028	-9.5447	24.6095	-50.9984
8	8.3414	10.2675	-1.7342	18.2944	0.5199	1.6064	-0.1131	0.5506	-0.2717	-0.155	0.4387	-0.2474	-0.1005	0.4593	-0.3256	-0.0001	0.0006	-0.0004	-0.0006	0.0008	-0.0002	-36.8653	62.3441	-56.5093
9	1.9659	0.0117	0.5596	0.0426	0.4045	3.9472	0.0062	0.002	0.0929	0.086	0.0406	0.0777	-0.1303	0.2584	-0.0467	-0.0221	-0.0404	-0.0278	0.0189	0.0199	0.0256	-10.6303	24.0521	-119.0583
10	3.0092	4.2342	2.0209	10.8444	3.0922	2.4538	-0.2854	0.2666	0.0292	-0.4889	0.4645	-0.3194	-0.1017	0.5511	-0.1791	-0.0003	0.0011	-0.0011	-0.0002	0.001	-0.0003	-36.7863	63.2357	-125.0951
11	0.8171	0.3775	1.88	0.4904	2.044	8.6975	0.306	-0.1785	-0.1421	0.1664	-0.1578	-0.1854	0.3396	-0.6102	-0.1482	-0.0079	-0.0339	0.0421	-0.0127	0.0243	0.0063	-51.6075	-23.2513	-84.8769
12	1.2015	-4.183	-0.1932	14.5629	0.6728	0.0311	0.1888	0.599	0.5467	-0.8004	0.2547	0.5217	0.1636	-1.1016	-0.4435	-0.0003	-0.0001	0.0003	-0.0006	0.0007	-0.0003	-23.4133	-62.3576	-90.6308

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 499
2	X-RAY DIFFRACTION	1	A	998 - 999
3	X-RAY DIFFRACTION	2	B	2 - 496
4	X-RAY DIFFRACTION	2	B	998 - 999
5	X-RAY DIFFRACTION	3	C	3 - 497
6	X-RAY DIFFRACTION	3	C	998 - 999
7	X-RAY DIFFRACTION	4	D	2 - 496
8	X-RAY DIFFRACTION	4	D	998 - 999
9	X-RAY DIFFRACTION	5	E	2 - 497
10	X-RAY DIFFRACTION	5	E	998 - 999
11	X-RAY DIFFRACTION	6	F	3 - 496
12	X-RAY DIFFRACTION	6	F	998 - 999
13	X-RAY DIFFRACTION	7	G	1 - 5
14	X-RAY DIFFRACTION	8	H	1 - 5
15	X-RAY DIFFRACTION	9	I	1 - 5
16	X-RAY DIFFRACTION	10	J	1 - 5
17	X-RAY DIFFRACTION	11	K	2 - 5
18	X-RAY DIFFRACTION	12	L	2 - 5

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