PDB-8qos: Capra hircus reactive intermediate deaminase A - V25W

ID or keywords:

Entry

Database: PDB / ID: 8qos

Title

Capra hircus reactive intermediate deaminase A - V25W

Components

2-iminobutanoate/2-iminopropanoate deaminase

Keywords

UNKNOWN FUNCTION / Enzyme / deaminase

Function / homology

Function and homology information

2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / 2-iminobutanoate/2-iminopropanoate deaminase / : / mRNA destabilization / mRNA catabolic process / lipid metabolic process / peroxisome / RNA endonuclease activity, producing 3'-phosphomonoesters / Hydrolases; Acting on ester bonds ...
Similarity search - Function

Biological species

Capra hircus (goat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.01 Å

Authors

Rizzi, G. / Visentin, C. / Di Pisa, F. / Ricagno, S.

Funding support

Italy, 1items

Citation

Journal: To Be Published
Title: Capra hircus reactive intermediate deaminase A - V25W
Authors: Rizzi, G. / Visentin, C. / Di Pisa, F. / Ricagno, S.

History

Deposition	Sep 29, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 26, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8qos.cif.gz	385.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8qos.ent.gz	260.7 KB	Display	PDB format
PDBx/mmJSON format	8qos.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8qos_validation.pdf.gz	2.6 MB	Display	wwPDB validaton report
Full document	8qos_full_validation.pdf.gz	2.6 MB	Display
Data in XML	8qos_validation.xml.gz	36.8 KB	Display
Data in CIF	8qos_validation.cif.gz	53.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qo/8qos ftp://data.pdbj.org/pub/pdb/validation_reports/qo/8qos	HTTPS FTP

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Related structure data

Similar structure data	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
Related items in Molecule of the Month	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (1)

Deposited unit

A: 2-iminobutanoate/2-iminopropanoate deaminase

B: 2-iminobutanoate/2-iminopropanoate deaminase

C: 2-iminobutanoate/2-iminopropanoate deaminase

D: 2-iminobutanoate/2-iminopropanoate deaminase

E: 2-iminobutanoate/2-iminopropanoate deaminase

F: 2-iminobutanoate/2-iminopropanoate deaminase

hetero molecules

88.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 2-iminobutanoate/2-iminopropanoate deaminase

B: 2-iminobutanoate/2-iminopropanoate deaminase

C: 2-iminobutanoate/2-iminopropanoate deaminase

hetero molecules

defined by author
Evidence: gel filtration
44.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: 2-iminobutanoate/2-iminopropanoate deaminase

E: 2-iminobutanoate/2-iminopropanoate deaminase

F: 2-iminobutanoate/2-iminopropanoate deaminase

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.350, 72.669, 106.772
Angle α, β, γ (deg.)	90.000, 100.950, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 5 or resid 8 or resid...
d_2	ens_1	(chain "B" and (resid 5 or resid 8 or resid...
d_3	ens_1	(chain "C" and (resid 5 or resid 8 or resid...
d_4	ens_1	(chain "D" and (resid 5 or resid 8 or resid...
d_5	ens_1	(chain "E" and (resid 5 or resid 8 or resid...
d_6	ens_1	(chain "F" and (resid 5 or resid 8 or resid...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-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
d_1	1	VAL	VAL	VAL	VAL	A	A	5	8
d_1	2	ILE	ILE	ILE	ILE	A	A	8	11
d_1	3	THR	THR	TYR	TYR	A	A	11 - 21	14 - 24
d_1	4	GLN	GLN	GLY	GLY	A	A	23 - 44	26 - 47
d_1	5	LEU	LEU	VAL	VAL	A	A	46 - 77	49 - 80
d_1	6	ALA	ALA	ILE	ILE	A	A	79 - 86	82 - 89
d_1	7	ASP	ASP	SER	SER	A	A	88 - 102	91 - 105
d_1	8	PHE	PHE	PRO	PRO	A	A	104 - 116	107 - 119
d_1	9	GLY	GLY	PRO	PRO	A	A	118 - 131	121 - 134
d_2	1	VAL	VAL	VAL	VAL	B	B	5	8
d_2	2	ILE	ILE	ILE	ILE	B	B	8	11
d_2	3	THR	THR	TYR	TYR	B	B	11 - 21	14 - 24
d_2	4	GLN	GLN	GLY	GLY	B	B	23 - 44	26 - 47
d_2	5	LEU	LEU	VAL	VAL	B	B	46 - 77	49 - 80
d_2	6	ALA	ALA	ILE	ILE	B	B	79 - 86	82 - 89
d_2	7	ASP	ASP	SER	SER	B	B	88 - 102	91 - 105
d_2	8	PHE	PHE	PRO	PRO	B	B	104 - 116	107 - 119
d_2	9	GLY	GLY	PRO	PRO	B	B	118 - 131	121 - 134
d_3	1	VAL	VAL	VAL	VAL	C	C	5	8
d_3	2	ILE	ILE	ILE	ILE	C	C	8	11
d_3	3	THR	THR	TYR	TYR	C	C	11 - 21	14 - 24
d_3	4	GLN	GLN	GLY	GLY	C	C	23 - 44	26 - 47
d_3	5	LEU	LEU	VAL	VAL	C	C	46 - 77	49 - 80
d_3	6	ALA	ALA	ILE	ILE	C	C	79 - 86	82 - 89
d_3	7	ASP	ASP	SER	SER	C	C	88 - 102	91 - 105
d_3	8	PHE	PHE	PRO	PRO	C	C	104 - 116	107 - 119
d_3	9	GLY	GLY	PRO	PRO	C	C	118 - 131	121 - 134
d_4	1	VAL	VAL	VAL	VAL	D	D	5	8
d_4	2	ILE	ILE	ILE	ILE	D	D	8	11
d_4	3	THR	THR	TYR	TYR	D	D	11 - 21	14 - 24
d_4	4	GLN	GLN	GLY	GLY	D	D	23 - 44	26 - 47
d_4	5	LEU	LEU	VAL	VAL	D	D	46 - 77	49 - 80
d_4	6	ALA	ALA	ILE	ILE	D	D	79 - 86	82 - 89
d_4	7	ASP	ASP	SER	SER	D	D	88 - 102	91 - 105
d_4	8	PHE	PHE	PRO	PRO	D	D	104 - 116	107 - 119
d_4	9	GLY	GLY	PRO	PRO	D	D	118 - 131	121 - 134
d_5	1	VAL	VAL	VAL	VAL	E	E	5	8
d_5	2	ILE	ILE	ILE	ILE	E	E	8	11
d_5	3	THR	THR	TYR	TYR	E	E	11 - 21	14 - 24
d_5	4	GLN	GLN	GLY	GLY	E	E	23 - 44	26 - 47
d_5	5	LEU	LEU	VAL	VAL	E	E	46 - 77	49 - 80
d_5	6	ALA	ALA	ILE	ILE	E	E	79 - 86	82 - 89
d_5	7	ASP	ASP	SER	SER	E	E	88 - 102	91 - 105
d_5	8	PHE	PHE	PRO	PRO	E	E	104 - 116	107 - 119
d_5	9	GLY	GLY	PRO	PRO	E	E	118 - 131	121 - 134
d_6	1	VAL	VAL	VAL	VAL	F	F	5	8
d_6	2	ILE	ILE	ILE	ILE	F	F	8	11
d_6	3	THR	THR	TYR	TYR	F	F	11 - 21	14 - 24
d_6	4	GLN	GLN	GLY	GLY	F	F	23 - 44	26 - 47
d_6	5	LEU	LEU	VAL	VAL	F	F	46 - 77	49 - 80
d_6	6	ALA	ALA	ILE	ILE	F	F	79 - 86	82 - 89
d_6	7	ASP	ASP	SER	SER	F	F	88 - 102	91 - 105
d_6	8	PHE	PHE	PRO	PRO	F	F	104 - 116	107 - 119
d_6	9	GLY	GLY	PRO	PRO	F	F	118 - 131	121 - 134

#1: Protein	2-iminobutanoate/2-iminopropanoate deaminase Mass: 14678.714 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Capra hircus (goat) / Gene: RIDA / Production host: Escherichia coli (E. coli) / References: UniProt: P80601
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.54 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Potassium thiocyanate, 30% w/v PEG 2000 MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
Detector	Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 31, 2021
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.968 Å / Relative weight: 1
Reflection	Resolution: 2.01→59.72 Å / Num. obs: 61313 / % possible obs: 98 % / Redundancy: 1.9 % / B_iso Wilson estimate: 26.46 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.125 / R_rim(I) all: 0.136 / Net I/σ(I): 9.3
Reflection shell	Resolution: 2.01→2.06 Å / Num. unique obs: 2936 / CC_1/2: 0.446

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
Aimless		data scaling
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.01→37.42 Å / SU ML: 0.2982 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1142
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2845	2603	4.94 %
R_work	0.2379	50038	-
obs	0.2402	52641	97.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 32.66 Å²

Refinement step

Cycle: LAST / Resolution: 2.01→37.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5805	0	23	627	6455

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0031	5989
X-RAY DIFFRACTION	f_angle_d	0.6509	8157
X-RAY DIFFRACTION	f_chiral_restr	0.0458	956
X-RAY DIFFRACTION	f_plane_restr	0.0048	1062
X-RAY DIFFRACTION	f_dihedral_angle_d	7.64	864

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	A	X-RAY DIFFRACTION	Torsion NCS	0.760882911813
ens_1	d_3	A	A	X-RAY DIFFRACTION	Torsion NCS	1.25461852277
ens_1	d_4	A	A	X-RAY DIFFRACTION	Torsion NCS	0.525444321051
ens_1	d_5	A	A	X-RAY DIFFRACTION	Torsion NCS	0.648978110855
ens_1	d_6	A	A	X-RAY DIFFRACTION	Torsion NCS	0.890184928846

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.01-2.04	0.3395	139	0.3675	2635	X-RAY DIFFRACTION	98.37
2.04-2.08	0.372	159	0.3149	2614	X-RAY DIFFRACTION	98.44
2.08-2.12	0.3253	130	0.2885	2627	X-RAY DIFFRACTION	98.5
2.12-2.17	0.2938	140	0.2934	2631	X-RAY DIFFRACTION	98.82
2.17-2.22	0.3479	140	0.298	2657	X-RAY DIFFRACTION	98.42
2.22-2.28	0.3016	130	0.2734	2625	X-RAY DIFFRACTION	97.97
2.28-2.34	0.3145	154	0.2723	2551	X-RAY DIFFRACTION	95.58
2.34-2.41	0.3255	132	0.2616	2466	X-RAY DIFFRACTION	92.89
2.41-2.49	0.3357	126	0.2559	2344	X-RAY DIFFRACTION	87.87
2.49-2.57	0.3158	145	0.2589	2549	X-RAY DIFFRACTION	95.63
2.57-2.68	0.3209	164	0.2631	2669	X-RAY DIFFRACTION	99.86
2.68-2.8	0.3411	132	0.2523	2687	X-RAY DIFFRACTION	99.79
2.8-2.95	0.2763	119	0.2434	2682	X-RAY DIFFRACTION	99.93
2.95-3.13	0.3267	117	0.2529	2737	X-RAY DIFFRACTION	99.86
3.13-3.37	0.3027	134	0.2351	2682	X-RAY DIFFRACTION	99.89
3.37-3.71	0.2389	141	0.2135	2666	X-RAY DIFFRACTION	99.75
3.71-4.25	0.2281	129	0.1976	2738	X-RAY DIFFRACTION	100
4.25-5.35	0.2046	141	0.1853	2735	X-RAY DIFFRACTION	99.86
5.35-37.42	0.2683	131	0.213	2743	X-RAY DIFFRACTION	98.83

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	2.22937646599	-0.798316998038	-0.270816731164	7.82481203667	3.756270981	9.15428569774	0.597118615424	-0.164398500119	0.827380516327	1.40457725988	-0.186598960422	1.15565237321	0.953343811171	-0.854386091588	-0.482259241565	0.441610432848	-0.139273998357	0.0831342481676	0.396993579361	-0.00871099357175	0.801290267306	-7.074	-10.584	9.36
2	1.31892002249	-0.957741761245	-0.637035984119	5.19171573443	3.21386477919	6.61403678371	0.0667775020909	-0.0564237234493	-0.345779724405	0.319237713544	0.0304847324604	0.0527406716498	0.415318489949	0.0543796281323	-0.0728069693377	0.164032956137	-0.0176014815639	-0.033824362557	0.157809505206	0.0364344869733	0.221182054306	3.317	-10.12	0.791
3	5.87896629234	-0.937508708125	-2.64450143287	5.48174070632	1.29930825188	4.73228875567	-0.0919939588132	0.287931598894	-0.654025957101	-0.592821325598	0.433712935036	0.542374604096	0.0666549650746	0.374607353828	-0.245785128589	0.189841332249	0.0448329111804	-0.070041681235	0.237195288715	-0.110068152621	0.408353533768	15.22	-10.295	-10.663
4	4.57585679625	0.132024163639	-1.21220931042	1.66076547842	-0.207649856236	1.26618900194	-0.0745588407611	0.0310667503877	0.249677471083	-0.148970628838	0.0642832927706	-0.0410498938576	-0.0204439825104	-0.00360689554541	0.021100838664	0.15913441325	0.00289538715743	-0.0157965547487	0.142720073368	-0.0192983939887	0.184820541876	8.185	-0.956	-6.646
5	2.79582379677	3.06559616743	-1.63950369847	5.91134504427	-0.076529649864	3.15556954894	0.070490324043	0.921814971639	0.937190525039	-0.686257080777	0.215435162024	0.187147433252	-0.284497924541	-0.257316952139	-0.210793003282	0.287111066813	0.0186759757894	0.0331891276492	0.21147183221	0.0291171268311	0.229301425884	15.978	7.395	-9.629
6	1.13585809211	2.17949544004	-0.0741457915826	4.18254175578	-0.138741841324	0.00553615350365	0.378260578836	2.50495382141	0.209193208962	-2.29759407692	-0.540106164448	0.363221422298	0.313878030034	0.522357376177	0.129648280447	0.538175075763	0.193795471717	-0.0932319177232	1.00210951695	0.0966180096493	0.355287416196	3.985	10.27	-6.621
7	2.37256401762	-1.82069929624	-1.85313082263	2.40955701455	2.46916847972	2.41895599752	-0.020855965606	-0.448705703977	-0.0978500427631	-0.0596249248645	0.254228134944	-0.206734487667	-0.0555670861481	0.343665255824	-0.206188494758	0.126156340762	-0.0179369673675	0.00414817673233	0.233386128974	0.00391741645164	0.191557606566	16.762	-1.36	-0.755
8	1.68489463139	1.26743915114	-0.20025847722	0.953298162522	-0.0400836630482	1.96959882868	-0.105076437775	-0.240827885663	0.464537682513	-0.157480371088	0.231171152103	0.69301625763	-0.377267263394	-0.349850033921	0.0749857052142	0.180408313371	0.546202568623	-0.140421706643	0.438710311819	-0.271957727329	0.85149647704	-6.215	0.84	1.453
9	8.1427678681	6.75962790991	-2.79376486963	8.37494939689	-0.783232152253	6.08727458434	0.35649218141	0.560945032046	-0.27939340278	-0.191053739947	0.0712222595992	1.33347180578	0.24027195644	-1.03316016623	-0.34867789619	0.246363017252	0.00521711544062	-0.102409913842	0.359144330819	0.0607140523151	0.495819799441	-6.574	11.078	4.409
10	4.27271464286	-0.117508193229	-0.0273159727934	3.31349902396	0.0685786715445	4.41630134541	0.0656182962453	0.12926784286	0.339179192303	-0.0538260159975	-0.00192788091158	-0.04100680354	-0.22538102149	0.0226328764297	-0.0889423832411	0.154983512646	0.00656108227976	-0.0113685947852	0.138179606556	-0.0352172627955	0.173917729483	8.19	15.748	5.271
11	0.478101811494	-0.688932429888	-0.789784023676	6.44444194424	-2.36002795611	3.58454014568	-0.136582627603	0.706045540426	-0.27454616532	0.231381569757	0.0872806980291	-0.38067915673	-0.292382682786	0.694323473228	0.0044797942082	0.158519553977	-0.137649762604	0.0305990606097	0.35746410178	-0.0281636973582	0.301020670086	24.901	22.853	6.878
12	5.62972894242	-0.583957508838	0.0863579986857	1.13428242434	0.218210713063	1.47471637906	-0.027784495373	-0.246579338105	0.29258604109	0.0620805202556	0.0592297332067	0.100482004982	-0.0158746642199	0.0750625504303	-0.0307055956051	0.21638893986	-0.00802685487528	-0.00257317235387	0.17105534231	0.00470063252256	0.129317110949	13.516	14.992	14.614
13	4.10334726081	0.240174137539	-0.718312671327	1.71209624882	1.54125060716	3.0575647343	0.0176759793807	-0.0150037248295	0.0299686895516	0.382481997627	0.0250852502658	-0.203785356599	0.0917279875825	0.278356580728	-0.0564889022299	0.25217373585	0.0161758373789	-0.0649065385943	0.186628837969	0.0276037160274	0.194354914124	20.006	11.196	21.891
14	3.45471210897	2.26878089118	-1.45068042992	1.50135578368	-0.556157210591	1.70125366678	0.0518890634503	-0.189931872186	0.0494651340053	0.0973955082007	0.0322549294917	-0.0926224738876	0.224146656934	0.260731601343	-0.0925985160108	0.211862049961	0.0263199956121	-0.00727286475031	0.222230440685	-0.0598184188345	0.226433893666	19.136	7.888	9.907
15	1.73580203106	2.04972812992	2.20745692553	2.41832022261	2.60663930163	2.80769592156	0.729214556694	-1.05080437469	1.12055318503	2.19770776833	-0.0107642105623	2.47832876235	-2.19026634442	-2.59936336519	-0.715309027938	0.761904553182	0.118101588579	0.321598100761	0.728273777601	0.131081019862	0.538112075629	-5.723	12.847	19.649
16	3.09362174674	3.645209006	-4.17260089579	7.34397146036	-3.17229563676	7.18886080589	-0.101930387209	-0.8091249402	-0.245251702446	0.937211690294	-0.246994983221	-0.384453111905	0.533799642042	-0.133735286096	0.341361633882	0.440720611736	0.0178076706722	0.00508652772669	0.312294139955	0.0159978537394	0.35476531971	10.111	-0.147	27.513
17	3.16211885874	-0.673225406977	0.371252829226	5.0534155289	-1.25615503402	4.5274240759	0.289416536787	-0.484832958224	-0.214606123499	0.240824946363	0.0711431975703	-0.00678431564864	0.267344762708	0.220410731351	-0.355082627672	0.272439649135	-0.000367040469139	-0.0723414230189	0.252531964998	0.0187488945161	0.157132870794	9.809	-3.894	21.932
18	4.48864417882	0.230511499052	-1.47676412513	1.27412406936	0.366520704693	1.94348015146	0.0205350443617	-0.170035206168	-0.541088416089	0.333132762878	-0.0144230664418	-0.256514787249	0.405362280373	0.21094533742	-0.0117091167683	0.342578182329	0.0600580944603	-0.0579995107709	0.203028400123	0.0574191333145	0.325228490136	16.287	-13.355	15.958
19	2.00314385241	-3.64390641615	6.03189331644	4.63245658283	-0.121838092752	4.86210180569	0.337376505302	-1.52742871664	-1.36607706544	1.95149533339	0.00105173511299	-1.16210486358	2.25743849978	0.555220602915	-0.330841421322	0.725708436469	0.23430471879	-0.171065064552	0.481114900115	0.111417933596	0.471019165436	6.853	-18.336	9.934
20	3.94807990727	1.72000952492	-0.143046721591	2.74003138458	-0.381061229568	0.276993182222	0.104821915185	-0.166150171056	-0.366335170408	0.149793308434	0.0612494494347	-0.412056335411	0.281992403826	0.204170117623	-0.167022259067	0.202967640224	0.0712240820093	-0.0681264201416	0.278552417849	-0.0680960652775	0.24310083665	19.093	-5.627	12.086
21	6.96563530055	0.919505300646	-3.37072688848	4.42595141746	-1.41585142656	8.85322555827	0.126138754009	0.242861149212	-1.06714799611	0.153375423024	0.301025158543	0.814652772748	1.26563109233	-2.27135038637	-0.463901542445	0.580244212726	-0.134642556477	0.0726196873505	0.390938629749	0.164245183621	0.343484504636	-0.92	-9.561	18.776
22	5.17662281447	2.20543613608	0.444293011107	2.13247588916	1.59291335209	5.11676959889	0.642006931754	0.421144757234	0.464655107506	-1.17111726728	-0.515640036103	0.727650881039	0.10804202558	-0.340741839119	-0.164585765365	0.536045108532	0.135088481189	-0.127643780216	0.350024484765	0.0589915792247	0.585240144412	10.787	41.58	46.073
23	2.73072575618	-0.359656718191	-1.63268301048	3.41819767553	-2.87585483578	9.53896696052	0.106227665005	-0.27153754152	0.0287216712692	0.031322516163	-0.0390300831926	-0.108614458758	-0.171930166602	0.1318278615	-0.100425897891	0.201026059089	0.00918952822008	0.0685983565117	0.181809822731	-0.0689655791389	0.289298554196	24.351	44.796	56.401
24	9.63133338985	1.18000974559	3.13734843957	6.99467854232	3.33084241857	2.49880282367	-0.0229940610567	0.234452662245	-0.653834598718	-0.680632134816	-0.184178937314	0.146509062886	-0.448447410571	0.0871407014229	0.306177192735	0.242139122061	0.00699239200834	0.064640345012	0.260338382876	-0.0573593100363	0.286215150308	15.153	36.148	47.586
25	0.460478642521	0.733426351648	-1.12949923161	4.43067631167	1.28045873847	5.81142262534	0.020211047507	-0.571484720317	1.2760934002	-0.0198853667762	0.148703662394	-0.165807781228	-0.165101687387	-0.517617453804	-0.0960658558939	0.211287834373	0.0368039547197	0.0545286936306	0.373297473298	-0.16881262927	0.480990446471	29.313	41.071	61.769
26	6.57681707836	0.402422894362	1.55370277092	2.83573273232	0.0647083938446	0.784371391097	0.0297835567688	-0.263569209979	0.011212098358	0.304953462264	-0.00444981890266	-0.0438718225156	-0.0871059435262	0.0148941967482	-0.0244050799002	0.274005383855	-0.0207223541909	0.0211157470244	0.220969767417	-0.0440977993168	0.202094628823	27.771	35.786	63.932
27	6.66597488246	-1.42204697169	1.03531001321	2.84152888318	-0.432217874877	1.37135810685	0.321635570275	0.250694314294	-0.039252869474	0.188486935754	-0.201686389087	-0.0322405042219	-0.154469113741	0.135764365501	-0.126220791807	0.231491304508	-0.0811568656981	0.024731530488	0.268198507136	-0.042924945473	0.14699052531	24.309	28.162	55.339
28	6.02030259286	-5.39693121355	-4.86840163985	6.37408650099	3.46225416597	7.42840675612	-0.020036848809	-0.899400171719	-0.102300498456	0.215110111438	0.124943019459	0.411129693156	-0.237587254115	0.301384102703	-0.00692993711925	0.250459720164	0.0171124305729	-0.00790099705497	0.177042466987	-0.0269100277383	0.22791684253	32.621	23.042	62.28
29	0.839335353486	-0.954821802556	0.795971697316	2.68754511238	0.793038494254	2.60153465683	-0.00826411659008	-1.0619968627	-0.0626221669952	0.49459432869	-0.195589787398	0.294972830324	0.420526534726	0.365005977862	0.076603597762	0.260959893635	-0.00563307242973	0.122323984551	0.357402438476	-0.074200441417	0.220392031309	26.941	22.423	55.35
30	4.02569103234	1.13739311967	2.78397395476	1.1072526957	0.721657421709	3.3489837337	0.206158669195	0.379600907321	0.285939449416	0.0223496522217	-0.0973326880671	-0.154003936807	-0.176214701395	0.313509078434	-0.0817988809518	0.202161859211	-0.0228933529742	0.0973579220381	0.193156424646	-0.0105354917636	0.26853171635	32.95	34.128	54.222
31	6.41711744007	5.2943336161	1.52004421239	4.75006125554	0.853850657724	0.778716008994	1.14754820881	0.440397467093	0.524609692251	0.785120191997	-0.24915909906	2.0250881841	0.227953353312	0.468795881448	-0.757592647906	0.688334129376	-0.325299518633	0.0894824356845	1.03093583958	-0.201112456519	0.765381814969	6.882	27.709	51.822
32	3.71821992421	-4.39135023425	0.809925082986	6.36291301333	-1.15096754884	8.42228860322	0.589758878459	0.0915587072037	0.689964374037	0.100122535778	-0.779986416666	0.685532511377	-0.64232783676	-0.0766008137502	0.200319940546	0.259455811394	-0.0123311755337	0.0573044492688	0.283049063924	-0.0337360983298	0.465867546754	10.265	19.782	47.983
33	3.78635507566	-1.28303668315	-0.452249421311	2.700475502	0.477355025762	3.66123349818	-0.153568700326	-0.220756140563	-0.206548103437	0.190903783893	0.163129721616	0.107833337795	0.066755922804	-0.243825164926	-0.0448404960969	0.18187005334	-0.0304372226954	0.0392162445314	0.133126309985	0.0135252567462	0.127755010609	24.68	14.917	47.08
34	5.25006723063	-0.154747539801	-0.352013786771	0.333246368259	-0.134596709805	0.913400646348	0.0566100531496	-0.0323558585981	-0.464203355294	-0.0841981337923	-0.00354830921941	-0.03170361332	0.212455059999	0.0200267476652	-0.0567601214539	0.220648324047	-0.00901605327082	0.024501817755	0.147391604783	0.00850887091547	0.157366782865	31.841	14.57	38.97
35	9.63229103036	3.04121413209	6.18719452618	2.5474832898	2.63144506969	7.65826633355	0.474490426282	0.442604439394	0.179443396992	-0.0332832391095	0.054733597549	-0.33409570983	-0.0546832996741	0.51191705008	-0.530618992346	0.276529270493	0.0121808253066	0.115926326154	0.208604409182	0.00695669818227	0.263408226347	39.466	19.403	31.564
36	6.15398917477	-5.82718971042	-6.80374279554	7.28440018455	4.75254295367	9.14147771365	0.232673873541	1.0690039003	-0.532851572151	-1.0657217957	0.343793378792	0.320397038389	-0.282814993177	-0.522435223087	-0.537645700401	0.316015162909	-0.0481021326776	-0.0077063994016	0.368580247678	-0.080099616171	0.226304562775	27.753	20.644	27.107
37	6.75182011553	-0.402292567464	3.48036374093	0.540574206552	0.501939708832	2.73138858393	0.166014727809	0.387647044082	0.0643613866125	0.0504176115041	-0.158271359163	0.0166018062995	0.471252668597	0.585066443007	0.0558260330302	0.228822072045	0.029727837646	0.084092747374	0.197137763079	-0.0276885770112	0.194518176168	39.698	23.725	43.561
38	8.47181239205	0.0587204931477	7.41360659531	3.61305637668	-0.236020118639	8.14483090884	-0.390050669255	-0.0568094120562	-0.150413091128	-0.230963114372	0.202416037411	0.0137278133182	-0.468098458113	-0.193995213187	0.281354934253	0.239393364394	-0.0343847050672	0.0444138072671	0.27579519339	0.00394713877495	0.106181713628	21.831	21.416	36.889
39	6.56241020571	5.40613508152	-5.94719641914	5.4315635951	-3.93812536976	6.36646907711	-0.385021821045	1.34328509244	-0.414248358089	-1.31437137097	0.855035393303	0.125521429475	0.00295005612003	-0.657664311026	-0.361120037554	0.510006384266	-0.0470786280109	-0.0916641160463	0.297663872368	0.0108455991347	0.48890651881	14.72	28.073	27.833
40	5.46354414556	-0.451039924932	-0.723358979731	7.18567177906	2.60434684345	1.35496242834	0.15080565311	0.942264990355	0.261056585704	-1.66133995654	-0.395209040056	-0.488054157097	0.0984396348336	-0.141574856345	0.193669216972	0.546992057952	0.0272101336119	0.115930416124	0.372087708342	0.00990371296339	0.233377695668	30.919	33.658	24.713
41	4.80303832187	2.29912672351	0.644838132288	2.75890130478	0.260248613917	2.57223520019	-0.184283041472	0.420916869317	0.147569945983	-0.158752940718	0.221449103752	-0.308169577087	-0.402974024189	0.249960582299	-0.0501499280139	0.385046551882	0.0248521630634	0.107999708526	0.262903742776	0.0183064709757	0.212535554189	31.122	40.071	31.015
42	6.24485691375	0.00672124492317	-0.364291843712	0.640181793466	-0.244276232123	1.55982421884	0.0711265078818	-0.0607630636295	0.347137036544	-0.0916200909688	0.139600984692	-0.144285306579	-0.564577884465	-0.00689694859225	-0.132995653267	0.429401941819	-0.0163713929133	0.10681971814	0.174654680274	-0.0262913186435	0.281810605812	31.458	44.647	41.618
43	5.40708230664	-0.777361275257	0.155952000277	0.403858458882	0.314072755891	1.46610434733	0.0192260974489	0.0629421692923	0.633171896057	-0.0370946535841	-0.0169111553003	-0.241374190843	-0.305366345789	0.12827534399	0.0153733520762	0.320289825426	-0.0529091228497	0.093951761829	0.183057276958	0.00828024352784	0.27226991012	32.91	39.464	41.514
44	5.25226044109	-5.64319513568	0.691613749179	6.22208236502	-0.626953842992	0.173369355697	0.795257603583	-1.0662396803	1.5094021957	-0.441133178781	0.602146212644	2.47626971295	-3.12077235135	-2.85303604919	-1.17477215148	0.677021517061	0.373321518185	0.231049987847	0.932762626018	-0.0810056719853	1.27151666627	11.396	40.748	33.741

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:9 )	A	1 - 9
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 10:33 )	A	10 - 33
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 34:50 )	A	34 - 50
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 51:85 )	A	51 - 85
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 86:99 )	A	86 - 99
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 100:105 )	A	100 - 105
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 106:128 )	A	106 - 128
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 129:131 )	A	129 - 131
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 2:9 )	B	2 - 9
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 10:43 )	B	10 - 43
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 44:50 )	B	44 - 50
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 51:85 )	B	51 - 85
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 86:105 )	B	86 - 105
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 106:128 )	B	106 - 128
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 129:132 )	B	129 - 132
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 5:23 )	C	5 - 23
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 24:43 )	C	24 - 43
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 44:99 )	C	44 - 99
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 100:105 )	C	100 - 105
20	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 106:128 )	C	106 - 128
21	X-RAY DIFFRACTION	21	( CHAIN C AND RESID 129:132 )	C	129 - 132
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 2:9 )	D	2 - 9
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 10:23 )	D	10 - 23
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 24:33 )	D	24 - 33
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 34:43 )	D	34 - 43
26	X-RAY DIFFRACTION	26	( CHAIN D AND RESID 44:69 )	D	44 - 69
27	X-RAY DIFFRACTION	27	( CHAIN D AND RESID 70:85 )	D	70 - 85
28	X-RAY DIFFRACTION	28	( CHAIN D AND RESID 86:99 )	D	86 - 99
29	X-RAY DIFFRACTION	29	( CHAIN D AND RESID 100:111 )	D	100 - 111
30	X-RAY DIFFRACTION	30	( CHAIN D AND RESID 112:128 )	D	112 - 128
31	X-RAY DIFFRACTION	31	( CHAIN D AND RESID 129:132 )	D	129 - 132
32	X-RAY DIFFRACTION	32	( CHAIN E AND RESID 2:9 )	E	2 - 9
33	X-RAY DIFFRACTION	33	( CHAIN E AND RESID 10:43 )	E	10 - 43
34	X-RAY DIFFRACTION	34	( CHAIN E AND RESID 44:85 )	E	44 - 85
35	X-RAY DIFFRACTION	35	( CHAIN E AND RESID 86:99 )	E	86 - 99
36	X-RAY DIFFRACTION	36	( CHAIN E AND RESID 100:105 )	E	100 - 105
37	X-RAY DIFFRACTION	37	( CHAIN E AND RESID 106:120 )	E	106 - 120
38	X-RAY DIFFRACTION	38	( CHAIN E AND RESID 121:133 )	E	121 - 133
39	X-RAY DIFFRACTION	39	( CHAIN F AND RESID 2:9 )	F	2 - 9
40	X-RAY DIFFRACTION	40	( CHAIN F AND RESID 10:23 )	F	10 - 23
41	X-RAY DIFFRACTION	41	( CHAIN F AND RESID 24:68 )	F	24 - 68
42	X-RAY DIFFRACTION	42	( CHAIN F AND RESID 69:99 )	F	69 - 99
43	X-RAY DIFFRACTION	43	( CHAIN F AND RESID 100:128 )	F	100 - 128
44	X-RAY DIFFRACTION	44	( CHAIN F AND RESID 129:131 )	F	129 - 131

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi