PDB-4aei: Crystal structure of the AaHII-Fab4C1 complex

ID or keywords:

Entry

Database: PDB / ID: 4aei

Title

Crystal structure of the AaHII-Fab4C1 complex

Components

(FAB ANTIBODY ...) x 2
ALPHA-MAMMAL TOXIN AAH2

Keywords

IMMUNE SYSTEM/TOXIN /

IMMUNE SYSTEM-TOXIN COMPLEX / ALPHA-TOXIN / CONFORMATIONAL REARRANGEMENT / COMBINING SITE /

EPITOPE / PHARMACOLOGICAL SITE /

VENOM / VOLTAGE-ACTIVATED SODIUM CHANNEL

Function / homology

Function and homology information

sodium channel inhibitor activity / defense response /

toxin activity / extracellular region
Similarity search - Function

Biological species

ANDROCTONUS AUSTRALIS HECTOR (scorpion)

MUS MUSCULUS (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Fabrichny, I.P. / Mondielli, G. / Conrod, S. / Martin-Eauclaire, M.F. / Bourne, Y. / Marchot, P.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Structural Insights Into Antibody Sequestering and Neutralizing of Na+-Channel & [Alpha]-Type Modulator from Old-World Scorpion Venom
Authors: Fabrichny, I.P. / Mondielli, G. / Conrod, S. / Martin-Eauclaire, M.F. / Bourne, Y. / Marchot, P.

History

Deposition	Jan 10, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 7, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 2, 2012	Group: Other
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...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 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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	4aei.cif.gz	583.7 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ae/4aei ftp://data.pdbj.org/pub/pdb/validation_reports/ae/4aei	HTTPS FTP

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Related structure data

Related structure data	4aehC 1ptxS 1aho 1seg S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6a77-d 4lmq-1 6b0s-d 4k34-2 6ywd-d 6ddm-d 6bfq-1 4ffz-2 4dn4-d 1ztx-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) 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #199 - Jul 2016 Monellin similarity (1) #38 - Feb 2003 Potassium Channels similarity (1)

Deposited unit

A: ALPHA-MAMMAL TOXIN AAH2

B: ALPHA-MAMMAL TOXIN AAH2

C: ALPHA-MAMMAL TOXIN AAH2

H: FAB ANTIBODY HEAVY CHAIN

I: FAB ANTIBODY HEAVY CHAIN

J: FAB ANTIBODY HEAVY CHAIN

L: FAB ANTIBODY LIGHT CHAIN

M: FAB ANTIBODY LIGHT CHAIN

N: FAB ANTIBODY LIGHT CHAIN

hetero molecules

169 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ALPHA-MAMMAL TOXIN AAH2

H: FAB ANTIBODY HEAVY CHAIN

L: FAB ANTIBODY LIGHT CHAIN

hetero molecules

defined by author&software
56.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ALPHA-MAMMAL TOXIN AAH2

I: FAB ANTIBODY HEAVY CHAIN

M: FAB ANTIBODY LIGHT CHAIN

hetero molecules

defined by author&software
56.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: ALPHA-MAMMAL TOXIN AAH2

J: FAB ANTIBODY HEAVY CHAIN

N: FAB ANTIBODY LIGHT CHAIN

hetero molecules

defined by author&software
56.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	123.940, 38.740, 154.070
Angle α, β, γ (deg.)	90.00, 91.36, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
1	2	L
2	2	N
3	2	M
1	3	L
2	3	N
3	3	M
1	4	H
2	4	J
3	4	I
1	5	H
2	5	J
3	5	I

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	VAL	VAL	NH2	NH2	A	A	1 - 65	1 - 65
2	1	VAL	VAL	NH2	NH2	B	B	1 - 65	1 - 65
3	1	VAL	VAL	NH2	NH2	C	C	1 - 65	1 - 65
1	2	ASP	ASP	ARG	ARG	L	G	1 - 113	1 - 113
2	2	ASP	ASP	ARG	ARG	N	I	1 - 113	1 - 113
3	2	ASP	ASP	ARG	ARG	M	H	1 - 113	1 - 113
1	3	ALA	ALA	ARG	ARG	L	G	114 - 216	114 - 216
2	3	ALA	ALA	ARG	ARG	N	I	114 - 216	114 - 216
3	3	ALA	ALA	ARG	ARG	M	H	114 - 216	114 - 216
1	4	GLU	GLU	ALA	ALA	H	D	1 - 120	1 - 120
2	4	GLU	GLU	ALA	ALA	J	F	1 - 120	1 - 120
3	4	GLU	GLU	ALA	ALA	I	E	1 - 120	1 - 120
1	5	ALA	ALA	LYS	LYS	H	D	121 - 216	121 - 216
2	5	ALA	ALA	LYS	LYS	J	F	121 - 216	121 - 216
3	5	ALA	ALA	LYS	LYS	I	E	121 - 216	121 - 216

NCS ensembles :

ID
1
2
3
4
5

NCS oper:

ID	Code	Matrix	Vector
1	given	(-1, 0.001352, 0.007041), (0.001362, 1, 0.001283), (-0.007039, 0.001293, -1)	121.7, -19.51, 51.64
2	given	(0.9992, -0.02029, -0.03379), (0.02051, 0.9998, 0.006323), (0.03365, -0.007011, 0.9994)	4.252, -40.48, -53.09
3	given	(-0.9996, -0.002625, -0.0295), (-0.002735, 1, 0.003689), (0.02949, 0.003768, -0.9996)	123.3, -19.08, 48.87
4	given	(0.9987, -0.04778, -0.01693), (0.04744, 0.9987, -0.02031), (0.01788, 0.01948, 0.9997)	4.276, -40.25, -53.31
5	given	(-0.9997, 0.000943, -0.02334), (0.000936, 1, 0.000311), (0.02334, 0.000289, -0.9997)	122.9, -19.37, 49.39
6	given	(-0.9961, 0.07033, -0.05353), (0.07031, 0.9975, 0.002336), (0.05356, -0.001437, -0.9986)	120.9, 14.11, 98.89

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Protein , 1 types, 3 molecules ABC

#1: Protein	ALPHA-MAMMAL TOXIN AAH2 / AAH II / AAHII / NEUROTOXIN 2 Mass: 7260.175 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ANDROCTONUS AUSTRALIS HECTOR (scorpion) / References: UniProt: P01484

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Antibody , 2 types, 6 molecules HIJLMN

#2: Antibody	FAB ANTIBODY HEAVY CHAIN Mass: 24701.740 Da / Num. of mol.: 3 / Fragment: VARIABLE DOMAIN / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#3: Antibody	FAB ANTIBODY LIGHT CHAIN Mass: 24117.709 Da / Num. of mol.: 3 / Fragment: VARIABLE DOMAIN / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)

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Non-polymers , 3 types, 219 molecules

#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	AMIDATED HIS64

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44 % / Description: NONE
Crystal grow	pH: 8 / Details: 15% PEG 2000 MME, 0.1 M HEPES PH 8.0, 0.1 M NACL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.3→13 Å / Num. obs: 65949 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 4 % / B_iso Wilson estimate: 34.6 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 10.8
Reflection shell	Resolution: 2.3→2.35 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 3.45 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PTX

1ptx

Resolution: 2.3→12.97 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.93 / SU B: 16.469 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.412 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25403	3298	5 %	RANDOM
R_work	0.19862	-	-	-
obs	0.20135	62651	99.23 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 45.863 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.58 Å²	-0 Å²	-2.39 Å²
2-	-	-0.47 Å²	0 Å²
3-	-	-	-0.23 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→12.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11436	0	51	210	11697

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.02	11986
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.365	1.953	16335
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.682	5	1508
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.588	23.685	502
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.718	15	1876
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.007	15	61
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	1771
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	9162
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

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	255	medium positional	0.07	0.5
1	2	B	255	medium positional	0.08	0.5
1	3	C	255	medium positional	0.06	0.5
2	1	L	443	medium positional	0.21	0.5
2	3	M	443	medium positional	0.13	0.5
2	2	N	443	medium positional	0.14	0.5
3	1	L	396	medium positional	0.21	0.5
3	3	M	396	medium positional	0.22	0.5
3	2	N	396	medium positional	0.2	0.5
4	1	H	472	medium positional	0.12	0.5
4	2	J	472	medium positional	0.16	0.5
4	3	I	472	medium positional	0.13	0.5
5	1	H	344	medium positional	0.2	0.5
5	2	J	344	medium positional	0.24	0.5
5	3	I	344	medium positional	0.29	0.5
1	1	A	257	loose positional	0.49	5
1	2	B	257	loose positional	0.61	5
1	3	C	257	loose positional	0.41	5
2	1	L	399	loose positional	0.61	5
2	3	M	399	loose positional	0.56	5
2	2	N	399	loose positional	0.53	5
3	1	L	371	loose positional	0.52	5
3	3	M	371	loose positional	0.54	5
3	2	N	371	loose positional	0.58	5
4	1	H	455	loose positional	0.37	5
4	2	J	455	loose positional	0.38	5
4	3	I	455	loose positional	0.43	5
5	1	H	290	loose positional	0.48	5
5	2	J	290	loose positional	0.55	5
5	3	I	290	loose positional	0.67	5
1	1	A	255	medium thermal	1.06	2
1	2	B	255	medium thermal	1.29	2
1	3	C	255	medium thermal	0.77	2
2	1	L	443	medium thermal	1.68	2
2	3	M	443	medium thermal	2.89	2
2	2	N	443	medium thermal	2.63	2
3	1	L	396	medium thermal	6.5	2
3	3	M	396	medium thermal	6.68	2
3	2	N	396	medium thermal	2.77	2
4	1	H	472	medium thermal	1.62	2
4	2	J	472	medium thermal	2.88	2
4	3	I	472	medium thermal	2.04	2
5	1	H	344	medium thermal	6.22	2
5	2	J	344	medium thermal	6.22	2
5	3	I	344	medium thermal	3.34	2
1	1	A	257	loose thermal	1.77	10
1	2	B	257	loose thermal	2.23	10
1	3	C	257	loose thermal	1.16	10
2	1	L	399	loose thermal	2.18	10
2	3	M	399	loose thermal	3.15	10
2	2	N	399	loose thermal	2.85	10
3	1	L	371	loose thermal	6.36	10
3	3	M	371	loose thermal	6.04	10
3	2	N	371	loose thermal	2.87	10
4	1	H	455	loose thermal	2.05	10
4	2	J	455	loose thermal	2.77	10
4	3	I	455	loose thermal	2.48	10
5	1	H	290	loose thermal	6.06	10
5	2	J	290	loose thermal	6.33	10
5	3	I	290	loose thermal	3.98	10

LS refinement shell

Resolution: 2.3→2.358 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.316	219	-
R_work	0.269	4200	-
obs	-	-	99.91 %

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	2.1517	0.0687	0.0456	1.9545	-0.4315	2.3903	-0.0355	0.0288	0.0891	-0.183	0.0901	0.1911	0.0364	-0.2871	-0.0546	0.1279	-0.0136	0.0267	0.0435	0.0097	0.0409	57.7666	15.3766	31.5451
2	2.7587	-0.2976	0.6397	2.1138	-0.0663	3.1449	0.0749	0.0627	0.0916	0.2313	-0.0639	-0.1379	-0.0805	0.2365	-0.011	0.173	-0.0184	0.0701	0.0513	0.0047	0.0593	63.0949	34.7074	70.9147
3	2.607	-0.132	0.577	2.4582	0.7654	3.0778	-0.0054	-0.0296	0.0829	0.0116	0.0457	-0.0239	-0.0695	0.208	-0.0403	0.1433	-0.0241	0.0117	0.0735	0.0122	0.011	64.2187	-4.0034	19.6871
4	2.2533	0.3844	0.6291	1.2944	-0.3535	0.8389	-0.1435	-0.0989	0.0376	0.0509	0.031	-0.1737	-0.0449	-0.0608	0.1125	0.0737	0.0369	0.0233	0.0451	-0.0193	0.0786	79.774	17.7184	47.9018
5	1.5508	0.3188	0.2884	1.5972	-0.3526	1.4213	-0.0141	-0.2173	0.0228	0.0783	-0.0571	-0.0527	-0.0031	0.0221	0.0713	0.0854	0.0245	-0.008	0.1116	0.0101	0.2338	109.8591	17.5694	64.367
6	2.4996	-0.6574	0.6757	1.4688	0.1258	1.5347	-0.0739	0.0652	0.0192	-0.0312	0.032	0.2826	0.0185	-0.0527	0.0419	0.0939	-0.0301	0.0547	0.0841	0.0265	0.1305	40.642	37.7566	55.3839
7	3.2223	-1.1112	-0.2339	1.7893	0.7917	1.7587	0.225	0.4629	-0.2077	-0.2048	-0.2062	0.1131	-0.0875	-0.1311	-0.0188	0.2106	0.0378	-0.0162	0.3616	0.0074	0.321	9.9788	39.7576	40.4435
8	2.5674	-0.3086	0.6016	1.3031	0.3119	1.915	-0.1882	0.1176	0.1015	-0.1363	0.0249	0.2588	-0.1232	-0.1657	0.1632	0.1658	-0.0221	-0.0779	0.1305	0.0278	0.0968	42.1409	-1.4595	3.3795
9	1.9192	-0.6986	0.6589	2.6964	1.2798	1.619	-0.1041	0.157	0.1052	-0.2181	-0.1527	0.3652	-0.0508	-0.4973	0.2568	0.4231	-0.0615	-0.194	0.7709	-0.0591	0.4395	12.0751	-1.012	-12.0954

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 65
2	X-RAY DIFFRACTION	2	B	1 - 65
3	X-RAY DIFFRACTION	3	C	1 - 65
4	X-RAY DIFFRACTION	4	L	1 - 113
5	X-RAY DIFFRACTION	4	H	1 - 120
6	X-RAY DIFFRACTION	5	L	114 - 218
7	X-RAY DIFFRACTION	5	H	121 - 220
8	X-RAY DIFFRACTION	6	M	1 - 113
9	X-RAY DIFFRACTION	6	I	1 - 120
10	X-RAY DIFFRACTION	7	M	114 - 217
11	X-RAY DIFFRACTION	7	I	121 - 219
12	X-RAY DIFFRACTION	8	N	1 - 113
13	X-RAY DIFFRACTION	8	J	1 - 120
14	X-RAY DIFFRACTION	9	N	114 - 217
15	X-RAY DIFFRACTION	9	J	121 - 218

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