PDB-3iqf: Structure of F420 dependent methylene-tetrahydromethanopterin deh...

ID or keywords:

Entry

Database: PDB / ID: 3iqf

Title

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin

Components

F420-dependent methylenetetrahydromethanopterin dehydrogenase

Keywords

OXIDOREDUCTASE / binary complex of protein and substrate / Methanogenesis / One-carbon metabolism

Function / homology

Function and homology information

methylenetetrahydromethanopterin dehydrogenase / methylenetetrahydromethanopterin dehydrogenase activity / methanogenesis, from carbon dioxide / ferredoxin hydrogenase activity / one-carbon metabolic process
Similarity search - Function

Biological species

Methanopyrus kandleri (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Ceh, K.E. / Demmer, U. / Warkentin, E. / Moll, J. / Thauer, R.K. / Shima, S. / Ermler, U.

Citation

Journal: Biochemistry / Year: 2009
Title: Structural basis of the hydride transfer mechanism in F(420)-dependent methylenetetrahydromethanopterin dehydrogenase
Authors: Ceh, K. / Demmer, U. / Warkentin, E. / Moll, J. / Thauer, R.K. / Shima, S. / Ermler, U.

History

Deposition	Aug 20, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 6, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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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Validation report

Summary document	3iqf_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	3iqf_full_validation.pdf.gz	3 MB	Display
Data in XML	3iqf_validation.xml.gz	132.5 KB	Display
Data in CIF	3iqf_validation.cif.gz	172.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iq/3iqf ftp://data.pdbj.org/pub/pdb/validation_reports/iq/3iqf	HTTPS FTP

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Related structure data

Related structure data	3iqeC 3iqzC 1qv9S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1qv9-1 1u6j-2 1u6i-1 1u6k-1 3iqe-d 1u6i-2 3iqz-d 1u6j-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: F420-dependent methylenetetrahydromethanopterin dehydrogenase

B: F420-dependent methylenetetrahydromethanopterin dehydrogenase

C: F420-dependent methylenetetrahydromethanopterin dehydrogenase

D: F420-dependent methylenetetrahydromethanopterin dehydrogenase

E: F420-dependent methylenetetrahydromethanopterin dehydrogenase

F: F420-dependent methylenetetrahydromethanopterin dehydrogenase

G: F420-dependent methylenetetrahydromethanopterin dehydrogenase

H: F420-dependent methylenetetrahydromethanopterin dehydrogenase

I: F420-dependent methylenetetrahydromethanopterin dehydrogenase

J: F420-dependent methylenetetrahydromethanopterin dehydrogenase

K: F420-dependent methylenetetrahydromethanopterin dehydrogenase

L: F420-dependent methylenetetrahydromethanopterin dehydrogenase

hetero molecules

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

1

A: F420-dependent methylenetetrahydromethanopterin dehydrogenase

B: F420-dependent methylenetetrahydromethanopterin dehydrogenase

C: F420-dependent methylenetetrahydromethanopterin dehydrogenase

D: F420-dependent methylenetetrahydromethanopterin dehydrogenase

E: F420-dependent methylenetetrahydromethanopterin dehydrogenase

F: F420-dependent methylenetetrahydromethanopterin dehydrogenase

hetero molecules

defined by author&software
193 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: F420-dependent methylenetetrahydromethanopterin dehydrogenase

H: F420-dependent methylenetetrahydromethanopterin dehydrogenase

I: F420-dependent methylenetetrahydromethanopterin dehydrogenase

J: F420-dependent methylenetetrahydromethanopterin dehydrogenase

K: F420-dependent methylenetetrahydromethanopterin dehydrogenase

L: F420-dependent methylenetetrahydromethanopterin dehydrogenase

hetero molecules

defined by author&software
193 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.400, 167.100, 122.500
Angle α, β, γ (deg.)	90.00, 113.60, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-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	1	THR	THR	ARG	ARG	3	B	B	2 - 84	2 - 84
2	1	1	THR	THR	ARG	ARG	3	A	A	2 - 84	2 - 84
3	1	1	THR	THR	ARG	ARG	3	C	C	2 - 84	2 - 84
4	1	1	THR	THR	ARG	ARG	3	D	D	2 - 84	2 - 84
5	1	1	THR	THR	ARG	ARG	3	F	F	2 - 84	2 - 84
1	2	1	SER	SER	GLU	GLU	3	B	B	90 - 170	90 - 170
2	2	1	SER	SER	GLU	GLU	3	A	A	90 - 170	90 - 170
3	2	1	SER	SER	GLU	GLU	3	C	C	90 - 170	90 - 170
4	2	1	SER	SER	GLU	GLU	3	D	D	90 - 170	90 - 170
5	2	1	SER	SER	GLU	GLU	3	F	F	90 - 170	90 - 170
1	3	1	ILE	ILE	GLU	GLU	3	B	B	173 - 283	173 - 283
2	3	1	ILE	ILE	GLU	GLU	3	A	A	173 - 283	173 - 283
3	3	1	ILE	ILE	GLU	GLU	3	C	C	173 - 283	173 - 283
4	3	1	ILE	ILE	GLU	GLU	3	D	D	173 - 283	173 - 283
5	3	1	ILE	ILE	GLU	GLU	3	F	F	173 - 283	173 - 283
1	1	2	THR	THR	PRO	PRO	3	B	B	2 - 46	2 - 46
2	1	2	THR	THR	PRO	PRO	3	E	E	2 - 46	2 - 46
1	2	2	ALA	ALA	ARG	ARG	3	B	B	51 - 84	51 - 84
2	2	2	ALA	ALA	ARG	ARG	3	E	E	51 - 84	51 - 84
1	3	2	SER	SER	GLU	GLU	3	B	B	90 - 170	90 - 170
2	3	2	SER	SER	GLU	GLU	3	E	E	90 - 170	90 - 170
1	4	2	ILE	ILE	GLU	GLU	4	B	B	173 - 283	173 - 283
2	4	2	ILE	ILE	GLU	GLU	4	E	E	173 - 283	173 - 283
1	1	3	GLU	GLU	ASP	ASP	3	D	D	85 - 89	85 - 89
2	1	3	GLU	GLU	ASP	ASP	3	A	A	85 - 89	85 - 89
3	1	3	GLU	GLU	ASP	ASP	3	C	C	85 - 89	85 - 89
4	1	3	GLU	GLU	ASP	ASP	3	E	E	85 - 89	85 - 89
5	1	3	GLU	GLU	ASP	ASP	3	F	F	85 - 89	85 - 89
1	1	4	THR	THR	GLU	GLU	3	L	L	2 - 170	2 - 170
2	1	4	THR	THR	GLU	GLU	3	G	G	2 - 170	2 - 170
3	1	4	THR	THR	GLU	GLU	3	I	I	2 - 170	2 - 170
4	1	4	THR	THR	GLU	GLU	3	J	J	2 - 170	2 - 170
1	2	4	ILE	ILE	GLU	GLU	3	L	L	173 - 283	173 - 283
2	2	4	ILE	ILE	GLU	GLU	3	G	G	173 - 283	173 - 283
3	2	4	ILE	ILE	GLU	GLU	3	I	I	173 - 283	173 - 283
4	2	4	ILE	ILE	GLU	GLU	3	J	J	173 - 283	173 - 283
1	1	5	THR	THR	PRO	PRO	3	L	L	2 - 46	2 - 46
2	1	5	THR	THR	PRO	PRO	3	H	H	2 - 46	2 - 46
1	2	5	ALA	ALA	GLU	GLU	3	L	L	51 - 170	51 - 170
2	2	5	ALA	ALA	GLU	GLU	3	H	H	51 - 170	51 - 170
1	3	5	ILE	ILE	GLU	GLU	3	L	L	173 - 283	173 - 283
2	3	5	ILE	ILE	GLU	GLU	3	H	H	173 - 283	173 - 283
1	1	6	THR	THR	ARG	ARG	3	L	L	2 - 84	2 - 84
2	1	6	THR	THR	ARG	ARG	3	K	K	2 - 84	2 - 84
1	2	6	SER	SER	GLU	GLU	3	L	L	90 - 170	90 - 170
2	2	6	SER	SER	GLU	GLU	3	K	K	90 - 170	90 - 170
1	3	6	ILE	ILE	GLU	GLU	3	L	L	173 - 283	173 - 283
2	3	6	ILE	ILE	GLU	GLU	3	K	K	173 - 283	173 - 283
1	1	7	ASP	ASP	GLU	GLU	1	E	E	171 - 172	171 - 172
2	1	7	ASP	ASP	GLU	GLU	1	A	A	171 - 172	171 - 172
3	1	7	ASP	ASP	GLU	GLU	1	B	B	171 - 172	171 - 172
4	1	7	ASP	ASP	GLU	GLU	1	C	C	171 - 172	171 - 172
5	1	7	ASP	ASP	GLU	GLU	1	D	D	171 - 172	171 - 172
6	1	7	ASP	ASP	GLU	GLU	1	F	F	171 - 172	171 - 172
7	1	7	ASP	ASP	GLU	GLU	1	G	G	171 - 172	171 - 172
8	1	7	ASP	ASP	GLU	GLU	1	H	H	171 - 172	171 - 172
9	1	7	ASP	ASP	GLU	GLU	1	I	I	171 - 172	171 - 172
10	1	7	ASP	ASP	GLU	GLU	1	J	J	171 - 172	171 - 172
11	1	7	ASP	ASP	GLU	GLU	1	K	K	171 - 172	171 - 172
12	1	7	ASP	ASP	GLU	GLU	1	L	L	171 - 172	171 - 172

NCS ensembles :

ID
1
2
3
4
5
6
7

#1: Protein	F420-dependent methylenetetrahydromethanopterin dehydrogenase / MTD / Coenzyme F420-dependent N5 / N10- methylenetetrahydromethanopterin dehydrogenase Mass: 31415.885 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: mtd / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P94951, EC: 1.5.99.9
#2: Chemical	ChemComp-E4M / 1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol Mass: 787.685 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃₁H₄₄N₆O₁₆P
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1068 / 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: 2.57 Å³/Da / Density % sol: 52.18 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG400, 0.1M MES, 0.1M sodium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.008 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2009
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.008 Å / Relative weight: 1
Reflection	Resolution: 2→112.5 Å / Num. all: 256709 / Num. obs: 246709 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / R_sym value: 0.062 / Net I/σ(I): 14.9
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 77.6 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 35779 / R_sym value: 0.511 / % possible all: 77.6

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.5.0066	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1QV9

1qv9

Resolution: 2.1→112.5 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.949 / SU B: 8.104 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.184 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20028	11021	5 %	RANDOM
R_work	0.16048	-	-	-
obs	0.16246	208672	99.23 %	-

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: 26.099 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.96 Å²	0 Å²	-0.06 Å²
2-	-	0.77 Å²	0 Å²
3-	-	-	0.014 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→112.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26184	0	548	1068	27800

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	27210
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	25076
X-RAY DIFFRACTION	r_angle_refined_deg	1.631	2.022	36845
X-RAY DIFFRACTION	r_angle_other_deg	0.949	3	58640
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.128	5	3386
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.654	25.584	1250
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.432	15	4889
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.253	15	168
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	4147
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	30009
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	4855
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	5976
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	26764
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	13486
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.2	16037
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.169	0.2	1358
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.079	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined	0.447	0.2	5
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.406	0.2	32
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.202	0.2	30
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.308	0.2	12
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.467	0.2	4
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.68	1.5	16965
X-RAY DIFFRACTION	r_mcbond_other	0.218	1.5	6775
X-RAY DIFFRACTION	r_mcangle_it	1.355	2	27294
X-RAY DIFFRACTION	r_scbond_it	2.65	3	10377
X-RAY DIFFRACTION	r_scangle_it	4.34	4.5	9544
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	B	1617	tight positional	0.04	0.05
1	2	A	1617	tight positional	0.04	0.05
1	3	C	1617	tight positional	0.04	0.05
1	4	D	1617	tight positional	0.04	0.05
1	5	F	1617	tight positional	0.04	0.05
2	1	B	937	tight positional	0.04	0.05
3	1	D	30	tight positional	0.03	0.05
3	2	A	30	tight positional	0.03	0.05
3	3	C	30	tight positional	0.03	0.05
3	4	E	30	tight positional	0.04	0.05
3	5	F	30	tight positional	0.03	0.05
4	1	L	1645	tight positional	0.05	0.05
4	2	G	1645	tight positional	0.04	0.05
4	3	I	1645	tight positional	0.05	0.05
4	4	J	1645	tight positional	0.05	0.05
5	1	L	1621	tight positional	0.05	0.05
6	1	L	1613	tight positional	0.06	0.05
7	1	E	27	tight positional	0.04	0.05
7	2	A	27	tight positional	0.05	0.05
7	3	B	27	tight positional	0.08	0.05
7	4	C	27	tight positional	0.04	0.05
7	5	D	27	tight positional	0.11	0.05
7	6	F	27	tight positional	0.19	0.05
7	7	G	27	tight positional	0.04	0.05
7	8	H	27	tight positional	0.06	0.05
7	9	I	27	tight positional	0.04	0.05
7	10	J	27	tight positional	0.04	0.05
7	11	K	27	tight positional	0.05	0.05
7	12	L	27	tight positional	0.18	0.05
2	1	B	1695	medium positional	0.17	0.5
1	1	B	2510	loose positional	0.33	5
1	2	A	2510	loose positional	0.32	5
1	3	C	2510	loose positional	0.3	5
1	4	D	2510	loose positional	0.32	5
1	5	F	2510	loose positional	0.31	5
2	1	B	1452	loose positional	0.23	5
3	1	D	43	loose positional	0.23	5
3	2	A	43	loose positional	0.3	5
3	3	C	43	loose positional	0.23	5
3	4	E	43	loose positional	0.28	5
3	5	F	43	loose positional	0.16	5
4	1	L	2549	loose positional	0.36	5
4	2	G	2549	loose positional	0.34	5
4	3	I	2549	loose positional	0.33	5
4	4	J	2549	loose positional	0.38	5
5	1	L	2522	loose positional	0.3	5
6	1	L	2495	loose positional	0.27	5
1	1	B	1617	tight thermal	0.21	0.5
1	2	A	1617	tight thermal	0.18	0.5
1	3	C	1617	tight thermal	0.18	0.5
1	4	D	1617	tight thermal	0.19	0.5
1	5	F	1617	tight thermal	0.17	0.5
2	1	B	937	tight thermal	0.18	0.5
3	1	D	30	tight thermal	0.09	0.5
3	2	A	30	tight thermal	0.1	0.5
3	3	C	30	tight thermal	0.1	0.5
3	4	E	30	tight thermal	0.09	0.5
3	5	F	30	tight thermal	0.08	0.5
4	1	L	1645	tight thermal	0.17	0.5
4	2	G	1645	tight thermal	0.15	0.5
4	3	I	1645	tight thermal	0.19	0.5
4	4	J	1645	tight thermal	0.16	0.5
5	1	L	1621	tight thermal	0.19	0.5
6	1	L	1613	tight thermal	0.2	0.5
7	1	E	27	tight thermal	0.07	0.5
7	2	A	27	tight thermal	0.06	0.5
7	3	B	27	tight thermal	0.05	0.5
7	4	C	27	tight thermal	0.05	0.5
7	5	D	27	tight thermal	0.07	0.5
7	6	F	27	tight thermal	0.07	0.5
7	7	G	27	tight thermal	0.04	0.5
7	8	H	27	tight thermal	0.06	0.5
7	9	I	27	tight thermal	0.09	0.5
7	10	J	27	tight thermal	0.05	0.5
7	11	K	27	tight thermal	0.07	0.5
7	12	L	27	tight thermal	0.08	0.5
2	1	B	1695	medium thermal	0.61	2
1	1	B	2510	loose thermal	1.27	10
1	2	A	2510	loose thermal	1.23	10
1	3	C	2510	loose thermal	1.24	10
1	4	D	2510	loose thermal	1.21	10
1	5	F	2510	loose thermal	1.37	10
2	1	B	1452	loose thermal	0.87	10
3	1	D	43	loose thermal	1.02	10
3	2	A	43	loose thermal	1.1	10
3	3	C	43	loose thermal	1.78	10
3	4	E	43	loose thermal	1.2	10
3	5	F	43	loose thermal	1.03	10
4	1	L	2549	loose thermal	1.27	10
4	2	G	2549	loose thermal	1.2	10
4	3	I	2549	loose thermal	1.25	10
4	4	J	2549	loose thermal	1.21	10
5	1	L	2522	loose thermal	0.99	10
6	1	L	2495	loose thermal	0.95	10

LS refinement shell

Resolution: 2.1→2.155 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.25	747	-
R_work	0.193	14359	-
obs	-	-	92.21 %

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	1.2346	-0.0584	0.2693	0.5185	0.0602	0.4971	-0.0797	0.0906	0.7001	-0.016	0.0186	-0.0723	-0.1773	0.0698	0.0611	0.0259	-0.0002	0.0164	-0.0354	0.0594	0.437	-6.405	27.066	43.73
2	1.4335	-0.0262	-0.0136	0.4806	0.171	0.6597	0.0614	0.2247	-0.1915	0.0332	-0.0372	0.084	0.1238	-0.1129	-0.0242	-0.023	0.0142	-0.0314	0.0365	-0.0401	0.0251	-27.111	-14.271	39.167
3	1.5368	0.0153	-0.0349	0.4115	0.0769	0.5706	0.0404	0.2401	-0.1063	0.0028	0.0365	-0.1173	0.0725	0.2415	-0.0769	-0.0284	0.0887	-0.0261	0.168	-0.0885	0.0485	19.386	-11.327	38.001
4	1.0253	0.0409	-0.145	0.5844	0.0511	0.7152	0.0973	0.0139	0.531	0.0056	0.0098	0.0452	-0.2835	0.0132	-0.1072	0.1622	0.0226	0.1247	-0.0588	0.0037	0.3502	20.045	25.884	98.873
5	0.9718	0.071	-0.0459	0.5571	0.083	0.6253	0.0273	0.0519	-0.0729	-0.0041	0.033	-0.1164	0.04	0.2158	-0.0603	-0.0071	0.0614	-0.0006	0.0644	-0.0562	0.0279	45.79	-12.544	94.295
6	0.8463	0.0783	-0.1156	0.5252	0.0492	0.6599	0.0295	0.0927	-0.0478	0.0077	-0.0299	0.1187	0.0954	-0.1384	0.0004	0.0003	0.0102	-0.0016	-0.0042	-0.0295	0.0482	-0.673	-15.721	95.562

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 283
2	X-RAY DIFFRACTION	1	D	2 - 283
3	X-RAY DIFFRACTION	2	B	2 - 283
4	X-RAY DIFFRACTION	2	F	2 - 283
5	X-RAY DIFFRACTION	3	C	2 - 283
6	X-RAY DIFFRACTION	3	E	2 - 283
7	X-RAY DIFFRACTION	4	G	2 - 283
8	X-RAY DIFFRACTION	4	J	2 - 283
9	X-RAY DIFFRACTION	5	H	2 - 283
10	X-RAY DIFFRACTION	5	L	2 - 283
11	X-RAY DIFFRACTION	6	I	2 - 283
12	X-RAY DIFFRACTION	6	K	2 - 283

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