PDB-1utd: The structure of the trp RNA-binding attenuation protein (TRAP) b...

ID or keywords:

Entry

Database: PDB / ID: 1utd

Title

The structure of the trp RNA-binding attenuation protein (TRAP) bound to a 63-nucleotide RNA molecule containing GAGUUU repeats

Components

5'-R(*GP*UP*UP*UP*GP*AP)-3'
TRANSCRIPTION ATTENUATION PROTEIN MTRB

Keywords

RNA BINDING PROTEIN / TRANSCRIPTION REGULATION / RNA-BINDING / TRP RNA TRANSCRIPTION ATTENUATION / RNA-BINDING PROTEIN

Function / homology

Function and homology information

DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / identical protein binding
Similarity search - Function

Biological species

BACILLUS STEAROTHERMOPHILUS (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Hopcroft, N.H. / Manfredo, A. / Wendt, A.L. / Brzozowski, A.M. / Gollnick, P. / Antson, A.A.

Citation

Journal: J.Mol.Biol. / Year: 2004
Title: The Interaction of RNA with Trap: The Role of Triplet Repeats and Separating Spacer Nucleotides
Authors: Hopcroft, N.H. / Manfredo, A. / Wendt, A.L. / Brzozowski, A.M. / Gollnick, P. / Antson, A.A.

History

Deposition	Dec 8, 2003	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 15, 2004	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Jul 27, 2011	Group: Other
Revision 1.3	Jun 5, 2013	Group: Derived calculations / Other / Refinement description
Revision 1.4	Aug 6, 2014	Group: Derived calculations / Other / Structure summary
Revision 1.5	Jul 29, 2020	Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Source and taxonomy Category: pdbx_database_status / pdbx_entity_src_syn ...pdbx_database_status / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / struct_site Item: _pdbx_database_status.status_code_sf / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_database_status.status_code_sf / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6	Dec 13, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1utd.cif.gz	353.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	1utd_validation.pdf.gz	680.6 KB	Display	wwPDB validaton report
Full document	1utd_full_validation.pdf.gz	712.1 KB	Display
Data in XML	1utd_validation.xml.gz	65.4 KB	Display
Data in CIF	1utd_validation.cif.gz	98.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ut/1utd ftp://data.pdbj.org/pub/pdb/validation_reports/ut/1utd	HTTPS FTP

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Related structure data

Related structure data	4v4fC 1c9sS 1gtf 1gtn 1qaw S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5eev-1 4v4f-2 5ef3-1 3aqd-2 1gtf-1 5eez-1 5eex-1 5ef2-1 1gtn-1 5ef1-1 5ef0-1 4v4f-4 1c9s-1 5eew-1 5eey-1 5eeu-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

0: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

1: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

2: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

3: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

4: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

5: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

6: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

7: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

8: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

9: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

A: TRANSCRIPTION ATTENUATION PROTEIN MTRB

B: TRANSCRIPTION ATTENUATION PROTEIN MTRB

C: TRANSCRIPTION ATTENUATION PROTEIN MTRB

D: TRANSCRIPTION ATTENUATION PROTEIN MTRB

E: TRANSCRIPTION ATTENUATION PROTEIN MTRB

F: TRANSCRIPTION ATTENUATION PROTEIN MTRB

G: TRANSCRIPTION ATTENUATION PROTEIN MTRB

H: TRANSCRIPTION ATTENUATION PROTEIN MTRB

I: TRANSCRIPTION ATTENUATION PROTEIN MTRB

J: TRANSCRIPTION ATTENUATION PROTEIN MTRB

K: TRANSCRIPTION ATTENUATION PROTEIN MTRB

L: TRANSCRIPTION ATTENUATION PROTEIN MTRB

M: TRANSCRIPTION ATTENUATION PROTEIN MTRB

N: TRANSCRIPTION ATTENUATION PROTEIN MTRB

O: TRANSCRIPTION ATTENUATION PROTEIN MTRB

P: TRANSCRIPTION ATTENUATION PROTEIN MTRB

Q: TRANSCRIPTION ATTENUATION PROTEIN MTRB

R: TRANSCRIPTION ATTENUATION PROTEIN MTRB

S: TRANSCRIPTION ATTENUATION PROTEIN MTRB

T: TRANSCRIPTION ATTENUATION PROTEIN MTRB

U: TRANSCRIPTION ATTENUATION PROTEIN MTRB

V: TRANSCRIPTION ATTENUATION PROTEIN MTRB

Z: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

hetero molecules

207 kDa, 33 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: TRANSCRIPTION ATTENUATION PROTEIN MTRB

B: TRANSCRIPTION ATTENUATION PROTEIN MTRB

C: TRANSCRIPTION ATTENUATION PROTEIN MTRB

D: TRANSCRIPTION ATTENUATION PROTEIN MTRB

E: TRANSCRIPTION ATTENUATION PROTEIN MTRB

F: TRANSCRIPTION ATTENUATION PROTEIN MTRB

G: TRANSCRIPTION ATTENUATION PROTEIN MTRB

H: TRANSCRIPTION ATTENUATION PROTEIN MTRB

I: TRANSCRIPTION ATTENUATION PROTEIN MTRB

J: TRANSCRIPTION ATTENUATION PROTEIN MTRB

K: TRANSCRIPTION ATTENUATION PROTEIN MTRB

hetero molecules

defined by author&software
93.1 kDa, 11 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

0: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

1: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

2: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

3: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

4: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

5: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

6: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

7: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

8: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

9: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

L: TRANSCRIPTION ATTENUATION PROTEIN MTRB

M: TRANSCRIPTION ATTENUATION PROTEIN MTRB

N: TRANSCRIPTION ATTENUATION PROTEIN MTRB

O: TRANSCRIPTION ATTENUATION PROTEIN MTRB

P: TRANSCRIPTION ATTENUATION PROTEIN MTRB

Q: TRANSCRIPTION ATTENUATION PROTEIN MTRB

R: TRANSCRIPTION ATTENUATION PROTEIN MTRB

S: TRANSCRIPTION ATTENUATION PROTEIN MTRB

T: TRANSCRIPTION ATTENUATION PROTEIN MTRB

U: TRANSCRIPTION ATTENUATION PROTEIN MTRB

V: TRANSCRIPTION ATTENUATION PROTEIN MTRB

Z: 5'-R(*GP*UP*UP*UP*GP*AP)-3'

hetero molecules

defined by author&software
114 kDa, 22 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	115.110, 134.230, 119.740
Angle α, β, γ (deg.)	90.00, 106.45, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2
3

Details

OLIGOMER OF 11 IDENTICAL PROTEIN SUBUNITS ARRANGED IN A DOUGHNUT-LIKE STRUCTURE WITH RNA CHAINS (0-9, Z) BOUND TO CHAINS L-V FORMING A 22MERIC STRUCTURE. NO RNA CONNECTED TO CHAINS A-K. HETGROUP TRP CONNECTED TO EACH PROTEIN CHAIN.

#1: RNA chain	5'-R(GPUPUPUPGPAP)-3' Mass: 1893.157 Da / Num. of mol.: 11 / Source method: obtained synthetically / Details: SYNTHETIC RNA. IN-VITRO TRANSCRIPTION / Source: (synth.) synthetic construct (others)
#2: Protein	... TRANSCRIPTION ATTENUATION PROTEIN MTRB / TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN / TRP RNA-BINDING ATTENUATION PROTEIN / TRAP Mass: 8257.377 Da / Num. of mol.: 22 Source method: isolated from a genetically manipulated source Details: TWO PROTEIN 11MERS (CHAINS A-K AND L-V) / Source: (gene. exp.) BACILLUS STEAROTHERMOPHILUS (bacteria) / Plasmid: PTZSTMTRB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG62052/PGP1-2 / References: UniProt: Q9X6J6
#3: Chemical	... ChemComp-TRP / TRYPTOPHAN Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 983 / Source method: isolated from a natural source / Formula: H₂O
Compound details	REQUIRED FOR TRANSCRIPTION REGULATION IN THE TRP OPERON. THIS TRANS-ACTING FACTOR SEEMS TO ...REQUIRED FOR TRANSCRIPTION REGULATION IN THE TRP OPERON. THIS TRANS-ACTING FACTOR SEEMS TO RECOGNIZE A 10 BASES NUCLEOTIDE SEQUENCE IN THE TRP LEADER TRANSCRIPT CAUSING TRANSCRIPTION TERMINATION.
Sequence details	63-NUCLEOTIDE RNA CONTAINING 11 GAG TRIPLETS SEPARATED BY UUU TRINUCLEOTIDES, RNA IS PRESENT IN ...63-NUCLEOTIDE RNA CONTAINING 11 GAG TRIPLETS SEPARATED BY UUU TRINUCLEOTIDES, RNA IS PRESENT IN RESIDUES 101-106 IN CHAINS Z, 0-9.

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Experiment

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

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Sample preparation

Crystal

Density Matthews: 2.19 Å³/Da / Density % sol: 43.85 %

Crystal grow

pH: 8
Details: 0.2M K-GLUTAMATE, 50 MM TRIETHANOLAMINE PH8.0, 10MM MGCL2, 8-11% MONOMETHYL ETHER PEG 2000+0.4M KCL AT END, pH 8.00

Crystal grow

*PLUS

pH: 7.8 / Method: vapor diffusion, hanging drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details	Chemical formula
1	15 mg/ml	RNA	1	drop
2	70 mM	potassium phosphate	1	drop	pH7.8
3	10 mM	L-tryptophan	1	drop
4	0.2 M	potassium glutamate	1	reservoir
5	50 mM	triethanolamine	1	reservoir	pH8.0
6	10 mM		1	reservoir		MgCl2
7	8-11 %(w/v)	PEG2000 MME	1	reservoir

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Data collection

Diffraction	Mean temperature: 120 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9336
Detector	Date: Jun 15, 2002
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9336 Å / Relative weight: 1
Reflection	Resolution: 2.1→30 Å / Num. obs: 99619 / % possible obs: 96.3 % / Redundancy: 3.3 % / R_merge(I) obs: 0.079 / Net I/σ(I): 15.2
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.254 / Mean I/σ(I) obs: 3.1 / % possible all: 76.8
Reflection	PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / Redundancy: 3.3 % / R_merge(I) obs*: 0.079
Reflection shell	PLUS % possible obs: 76.8 % / Redundancy: 2.2 % / Num. unique obs: 7922 / R_merge(I) obs: 0.254 / Mean I/σ(I) obs*: 3.1

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTYRY 1C9S

1c9s

Resolution: 2.1→20 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.932 / SU B: 4.71 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.228	986	1 %	RANDOM
R_work	0.169	-	-	-
obs	0.17	97170	100 %	-

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: 20.31 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.07 Å²	0 Å²	-0.54 Å²
2-	-	-0.77 Å²	0 Å²
3-	-	-	-0.61 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11996	815	330	983	14124

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.021	13375
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.488	1.999	18111
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.561	5	1526
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	2062
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	9650
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	5036
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	0.166	0.2	1206
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	0.256	0.2	32
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.167	0.2	41
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	0.826	1.5	7674
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.585	2.5	12291
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.923	4	5701
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.465	6	5820
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	279	tight positional	0.08	0.1
1	2	B	279	tight positional	0.09	0.1
1	3	C	279	tight positional	0.07	0.1
1	4	D	279	tight positional	0.09	0.1
1	5	E	279	tight positional	0.09	0.1
1	6	F	279	tight positional	0.07	0.1
1	7	G	279	tight positional	0.06	0.1
1	8	H	279	tight positional	0.06	0.1
1	9	I	279	tight positional	0.06	0.1
1	10	J	279	tight positional	0.07	0.1
1	11	K	279	tight positional	0.1	0.1
2	1	L	287	tight positional	0.12	0.1
2	2	M	287	tight positional	0.1	0.1
2	3	N	287	tight positional	0.08	0.1
2	4	O	287	tight positional	0.08	0.1
2	5	P	287	tight positional	0.06	0.1
2	6	Q	287	tight positional	0.13	0.1
2	7	R	287	tight positional	0.06	0.1
2	8	S	287	tight positional	0.06	0.1
2	9	T	287	tight positional	0.07	0.1
2	10	U	287	tight positional	0.06	0.1
2	11	V	287	tight positional	0.07	0.1
2	1	L	23	medium positional	0.28	0.3
2	2	M	23	medium positional	0.21	0.3
2	3	N	23	medium positional	0.47	0.3
2	4	O	23	medium positional	0.19	0.3
2	5	P	23	medium positional	0.19	0.3
2	6	Q	23	medium positional	0.16	0.3
2	7	R	23	medium positional	0.24	0.3
2	8	S	23	medium positional	0.11	0.3
2	9	T	23	medium positional	0.12	0.3
2	10	U	23	medium positional	0.15	0.3
2	11	V	23	medium positional	0.14	0.3
3	1	L	45	medium positional	0.36	0.3
3	2	N	45	medium positional	0.23	0.3
3	3	O	45	medium positional	0.27	0.3
3	4	P	45	medium positional	0.23	0.3
3	5	Q	45	medium positional	0.28	0.3
3	6	R	45	medium positional	0.2	0.3
3	7	S	45	medium positional	0.43	0.3
3	8	T	45	medium positional	0.49	0.3
3	9	U	45	medium positional	0.27	0.3
3	10	V	45	medium positional	0.19	0.3
1	1	A	249	loose positional	0.61	2
1	2	B	249	loose positional	0.57	2
1	3	C	249	loose positional	0.49	2
1	4	D	249	loose positional	0.86	2
1	5	E	249	loose positional	0.63	2
1	6	F	249	loose positional	0.58	2
1	7	G	249	loose positional	0.55	2
1	8	H	249	loose positional	0.95	2
1	9	I	249	loose positional	0.59	2
1	10	J	249	loose positional	0.61	2
1	11	K	249	loose positional	0.89	2
2	1	L	255	loose positional	0.54	2
2	2	M	255	loose positional	0.4	2
2	3	N	255	loose positional	0.31	2
2	4	O	255	loose positional	0.36	2
2	5	P	255	loose positional	0.33	2
2	6	Q	255	loose positional	0.35	2
2	7	R	255	loose positional	0.38	2
2	8	S	255	loose positional	0.36	2
2	9	T	255	loose positional	0.35	2
2	10	U	255	loose positional	0.29	2
2	11	V	255	loose positional	0.4	2
1	1	A	279	tight thermal	0.66	2
1	2	B	279	tight thermal	0.73	2
1	3	C	279	tight thermal	0.75	2
1	4	D	279	tight thermal	0.72	2
1	5	E	279	tight thermal	0.72	2
1	6	F	279	tight thermal	0.65	2
1	7	G	279	tight thermal	0.66	2
1	8	H	279	tight thermal	0.62	2
1	9	I	279	tight thermal	0.63	2
1	10	J	279	tight thermal	0.6	2
1	11	K	279	tight thermal	0.78	2
2	1	L	287	tight thermal	0.71	2
2	2	M	287	tight thermal	0.81	2
2	3	N	287	tight thermal	0.66	2
2	4	O	287	tight thermal	0.74	2
2	5	P	287	tight thermal	0.7	2
2	6	Q	287	tight thermal	0.58	2
2	7	R	287	tight thermal	0.62	2
2	8	S	287	tight thermal	0.64	2
2	9	T	287	tight thermal	0.69	2
2	10	U	287	tight thermal	0.56	2
2	11	V	287	tight thermal	0.63	2
2	1	L	23	medium thermal	3.66	5
2	2	M	23	medium thermal	2.39	5
2	3	N	23	medium thermal	3.98	5
2	4	O	23	medium thermal	3.38	5
2	5	P	23	medium thermal	2.92	5
2	6	Q	23	medium thermal	2.52	5
2	7	R	23	medium thermal	2.61	5
2	8	S	23	medium thermal	1.84	5
2	9	T	23	medium thermal	1.09	5
2	10	U	23	medium thermal	1.42	5
2	11	V	23	medium thermal	1.27	5
3	1	L	45	medium thermal	6.38	5
3	2	N	45	medium thermal	2.48	5
3	3	O	45	medium thermal	2.3	5
3	4	P	45	medium thermal	1.36	5
3	5	Q	45	medium thermal	2.33	5
3	6	R	45	medium thermal	1.35	5
3	7	S	45	medium thermal	1.74	5
3	8	T	45	medium thermal	2.86	5
3	9	U	45	medium thermal	1.63	5
3	10	V	45	medium thermal	2.81	5
1	1	A	249	loose thermal	2.56	5
1	2	B	249	loose thermal	2.39	5
1	3	C	249	loose thermal	1.95	5
1	4	D	249	loose thermal	2.54	5
1	5	E	249	loose thermal	2.03	5
1	6	F	249	loose thermal	2.16	5
1	7	G	249	loose thermal	1.98	5
1	8	H	249	loose thermal	1.64	5
1	9	I	249	loose thermal	1.69	5
1	10	J	249	loose thermal	1.77	5
1	11	K	249	loose thermal	2.54	5
2	1	L	255	loose thermal	1.81	5
2	2	M	255	loose thermal	1.71	5
2	3	N	255	loose thermal	1.69	5
2	4	O	255	loose thermal	1.5	5
2	5	P	255	loose thermal	1.9	5
2	6	Q	255	loose thermal	1.58	5
2	7	R	255	loose thermal	1.65	5
2	8	S	255	loose thermal	1.54	5
2	9	T	255	loose thermal	1.44	5
2	10	U	255	loose thermal	1.39	5
2	11	V	255	loose thermal	1.5	5

LS refinement shell

Resolution: 2.1→2.15 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.242	50
R_work	0.201	5731

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	4.1066	-1.9496	2.2328	2.0548	-1.4917	4.7879	0.0662	-0.0693	-0.0789	0.0372	0.0644	0.0838	0.1233	-0.009	-0.1306	0.0894	-0.0066	0.0483	0.0128	-0.022	0.0535	2.1696	-13.4001	55.2971
2	2.9841	-2.4767	1.8742	4.0055	-1.4366	5.4999	-0.0096	-0.1341	-0.0024	0.3519	0.0933	0.0428	0.0658	-0.2046	-0.0836	0.0966	-0.0326	0.0436	0.0189	-0.0127	0.0333	-1.2818	1.0417	56.8556
3	1.9405	-0.9096	1.485	4.1099	-1.6546	5.949	0.0019	-0.0459	0.0329	0.278	-0.0036	0.0263	-0.0032	-0.162	0.0017	0.0596	-0.0301	0.033	0.0226	-0.0219	0.0529	3.2253	15.3707	54.6773
4	0.9058	0.8803	0.1832	3.6552	-0.6661	6.2701	0.0187	0.0203	-0.0223	0.0899	-0.0314	0.018	-0.1411	-0.1213	0.0127	0.0159	-0.0132	0.006	0.0364	-0.0155	0.084	13.5507	24.8707	49.3193
5	1.8993	0.8005	-0.3679	1.5001	0.4844	6.9304	0.0079	-0.0008	0.008	-0.0356	0.0255	-0.0786	-0.2532	0.093	-0.0334	0.0109	-0.0228	-0.0124	0.0519	0.0036	0.1342	27.0228	26.0356	42.5998
6	3.1482	0.4237	0.0518	1.1851	1.0009	7.2119	-0.0142	0.0093	0.0029	-0.0452	0.0265	-0.211	-0.1445	0.1791	-0.0122	0.0158	-0.0068	-0.0003	0.0895	0.0158	0.1301	38.9427	19.1964	36.6367
7	3.1701	-0.2649	1.188	2.8204	2.3821	5.755	-0.104	0.0031	0.0592	-0.0301	0.0571	-0.202	0.0339	0.2901	0.0468	0.0052	0.0106	0.0151	0.1349	0.0218	0.1555	45.8074	6.2436	33.192
8	3.5809	0.0713	2.274	4.1311	1.5571	5.187	0.0388	0.1551	-0.085	0.0727	-0.0193	-0.2377	-0.0029	0.3011	-0.0195	0.0332	0.0497	0.0141	0.1377	0.0254	0.1481	45.236	-8.6775	33.2334
9	4.4839	1.2705	2.5552	3.5244	0.2661	4.6287	0.0728	0.1072	-0.1017	0.1425	-0.1001	-0.1806	0.1896	0.2843	0.0273	0.0853	0.0548	0.0283	0.1182	0.0399	0.118	37.4039	-20.9341	37.3838
10	5.7875	1.1702	2.807	2.2801	-0.0219	4.3029	0.1049	0.0785	-0.1623	0.028	-0.1507	-0.1635	0.3149	0.3486	0.0459	0.1043	0.0464	0.0644	0.0983	0.0307	0.0954	25.0694	-26.7629	43.4431
11	4.7381	-0.0258	0.9233	1.7853	-1.2957	3.8669	0.0289	0.0516	-0.0299	-0.0236	-0.0579	-0.0022	0.1141	0.1157	0.029	0.0857	0.0143	0.0135	0.0088	-0.0029	0.0607	11.8425	-23.8162	50.4082
12	3.0587	-1.0167	0.552	1.208	-0.0009	3.1175	0.0467	-0.0373	-0.1951	0.1639	0.0279	0.1672	0.4146	-0.1233	-0.0746	0.217	-0.0424	-0.0157	0.0932	-0.0097	0.1007	-9.424	-22.181	25.051
13	2.1526	-1.095	1.1044	2.4161	-0.1587	3.5375	0.1222	-0.0849	-0.1119	0.1446	0.0157	0.1341	0.218	-0.189	-0.1378	0.1185	-0.0644	0.0194	0.1073	0.0122	0.049	-15.973	-7.7764	27.332
14	1.9968	-1.0556	2.4496	4.0069	-1.1085	4.5008	-0.0228	-0.2374	0.0639	0.3036	0.0476	0.2127	-0.109	-0.4476	-0.0248	0.0656	-0.034	0.0419	0.1323	-0.0145	0.0683	-16.3779	8.1346	27.5476
15	1.6931	0.4717	1.5998	2.5768	-1.2856	5.3012	-0.0536	-0.1603	0.2342	0.2315	-0.045	0.1288	-0.3863	-0.3655	0.0987	0.0434	-0.0022	0.0389	0.1197	-0.0193	0.1052	-8.746	21.4294	23.6483
16	2.4977	0.7992	0.4189	0.96	-1.4737	6.4769	-0.0397	-0.1031	0.2897	0.13	-0.0545	-0.0423	-0.4524	-0.0169	0.0942	0.0518	-0.0034	0.0088	0.069	-0.0203	0.1173	4.3722	27.8077	17.1358
17	2.8571	-0.5012	0.044	1.4653	0.3111	5.6246	-0.0047	0.0434	0.291	-0.05	-0.0206	-0.2344	-0.3485	0.1941	0.0253	0.0202	-0.0194	0.0093	0.1065	0.0271	0.1362	18.3099	25.6003	10.0564
18	2.8568	-0.8226	0.6676	1.6924	1.5967	5.3276	-0.0229	0.2263	0.1782	-0.0211	0.0346	-0.2222	-0.1278	0.4217	-0.0117	0.0483	-0.0011	0.0111	0.1595	0.027	0.1084	29.0772	15.1087	4.564
19	1.2055	-0.308	0.8961	3.2024	1.7266	4.9447	-0.0103	0.1509	-0.0382	-0.0345	0.0946	-0.2921	0.062	0.5027	-0.0843	0.0491	0.036	0.0028	0.1895	-0.0027	0.1248	32.9039	-0.3402	2.7182
20	2.4678	1.3596	2.1493	3.4727	0.5917	4.5361	0.0864	0.1892	-0.3027	0.0676	-0.0108	-0.3001	0.2241	0.4273	-0.0756	0.1021	0.0729	0.0163	0.1679	-0.0186	0.1349	28.7421	-15.5422	4.8858
21	4.747	1.8741	1.8274	2.6695	-0.1278	3.4311	0.1729	0.0096	-0.4006	-0.0077	-0.0566	-0.1767	0.4516	0.1882	-0.1163	0.1843	0.0554	-0.0053	0.1195	-0.01	0.1087	17.9115	-25.8189	10.3583
22	4.0338	0.0168	0.7917	1.0856	-0.5203	3.5877	0.0256	-0.065	-0.2777	0.0545	-0.0208	-0.0183	0.4243	0.0716	-0.0047	0.2213	-0.0002	-0.0124	0.0851	-0.0072	0.1048	3.8821	-27.9252	17.439

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 74
2	X-RAY DIFFRACTION	1	A	81
3	X-RAY DIFFRACTION	2	B	5 - 75
4	X-RAY DIFFRACTION	2	B	81
5	X-RAY DIFFRACTION	3	C	5 - 74
6	X-RAY DIFFRACTION	3	C	81
7	X-RAY DIFFRACTION	4	D	5 - 75
8	X-RAY DIFFRACTION	4	D	81
9	X-RAY DIFFRACTION	5	E	5 - 74
10	X-RAY DIFFRACTION	5	E	81
11	X-RAY DIFFRACTION	6	F	5 - 74
12	X-RAY DIFFRACTION	6	F	81
13	X-RAY DIFFRACTION	7	G	5 - 74
14	X-RAY DIFFRACTION	7	G	81
15	X-RAY DIFFRACTION	8	H	5 - 75
16	X-RAY DIFFRACTION	8	H	81
17	X-RAY DIFFRACTION	9	I	5 - 74
18	X-RAY DIFFRACTION	9	I	81
19	X-RAY DIFFRACTION	10	J	5 - 75
20	X-RAY DIFFRACTION	10	J	81
21	X-RAY DIFFRACTION	11	K	5 - 74
22	X-RAY DIFFRACTION	11	K	81
23	X-RAY DIFFRACTION	12	L	5 - 75
24	X-RAY DIFFRACTION	12	L	81
25	X-RAY DIFFRACTION	13	M	5 - 74
26	X-RAY DIFFRACTION	13	M	81
27	X-RAY DIFFRACTION	14	N	5 - 74
28	X-RAY DIFFRACTION	14	N	81
29	X-RAY DIFFRACTION	15	O	5 - 75
30	X-RAY DIFFRACTION	15	O	81
31	X-RAY DIFFRACTION	16	P	5 - 74
32	X-RAY DIFFRACTION	16	P	81
33	X-RAY DIFFRACTION	17	Q	5 - 75
34	X-RAY DIFFRACTION	17	Q	81
35	X-RAY DIFFRACTION	18	R	5 - 75
36	X-RAY DIFFRACTION	18	R	81
37	X-RAY DIFFRACTION	19	S	5 - 74
38	X-RAY DIFFRACTION	19	S	81
39	X-RAY DIFFRACTION	20	T	5 - 74
40	X-RAY DIFFRACTION	20	T	81
41	X-RAY DIFFRACTION	21	U	5 - 74
42	X-RAY DIFFRACTION	21	U	81
43	X-RAY DIFFRACTION	22	V	5 - 74
44	X-RAY DIFFRACTION	22	V	81

Refinement

*PLUS

Highest resolution: 2.1 Å / Lowest resolution: 20 Å

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	r_bond_d	0.015	0.02
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.5	2

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