PDB-8dml: Vibrio parahaemolyticus VtrA/VtrC complex bound to the bile salt ...

ID or keywords:

Entry

Database: PDB / ID: 8dml

Title

Vibrio parahaemolyticus VtrA/VtrC complex bound to the bile salt chenodeoxycholate

Components

VtrA
VtrC

Keywords

SIGNALING PROTEIN / heterodimer / alpha/beta / calycin beta barrel superfamily / bile salt receptor / chenodeoxycholate

Function / homology

Function and homology information

phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / metal ion binding / membrane
Similarity search - Function

Biological species

Vibrio parahaemolyticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.08 Å

Model details

The C-terminal periplasmic domain of VtrA extends from residue 160 to 253. The C-terminal ...

Authors

Tomchick, D.R. / Orth, K. / Zou, A.J.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	130305	United States
Robert A. Welch Foundation	I-1561	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	S10OD025018	United States

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: Molecular determinants for differential activation of the bile acid receptor from the pathogen Vibrio parahaemolyticus.
Authors: Zou, A.J. / Kinch, L. / Chimalapati, S. / Garcia, N. / Tomchick, D.R. / Orth, K.

History

Deposition	Jul 8, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 14, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8dml.cif.gz	672.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8dml.ent.gz	468.5 KB	Display	PDB format
PDBx/mmJSON format	8dml.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dm/8dml ftp://data.pdbj.org/pub/pdb/validation_reports/dm/8dml	HTTPS FTP

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Related structure data

Related structure data	5kewS S: Starting model for refinement
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	#190 - Oct 2015 Two-component Systems similarity (4)

Deposited unit

A: VtrA

B: VtrC

C: VtrA

D: VtrC

E: VtrA

F: VtrC

G: VtrA

H: VtrC

hetero molecules

115 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: VtrA

B: VtrC

hetero molecules

defined by author&software
Evidence: gel filtration, homology
28.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: VtrA

D: VtrC

hetero molecules

defined by author&software
Evidence: gel filtration, immunoprecipitation
28.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: VtrA

F: VtrC

hetero molecules

defined by author&software
Evidence: gel filtration, homology
28.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: VtrA

H: VtrC

hetero molecules

defined by author&software
Evidence: gel filtration, homology
28.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	142.603, 41.763, 168.956
Angle α, β, γ (deg.)	90.000, 91.570, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein	VtrA Mass: 10982.484 Da / Num. of mol.: 4 / Fragment: VtrA C-terminal periplasmic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VPA1332 / Plasmid: pACYCDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q87GI4
#2: Protein	VtrC Mass: 16918.775 Da / Num. of mol.: 4 / Fragment: VtrC C-terminal periplasmic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VPA1333 / Plasmid: pACYCDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q87GI3

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Non-polymers , 5 types, 280 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-JN3 / CHENODEOXYCHOLIC ACID / (3ALPHA,5ALPHA,7BETA,8ALPHA,17ALPHA)-3,7-DIHYDROXYCHOLAN-24-OIC ACID Mass: 392.572 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₄H₄₀O₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.25 Å³/Da / Density % sol: 45.41 % / Mosaicity: 0.319 °
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 18% PEG 3350, 0.2 M calcium chloride, 10 mM Tris, 10 mM sodium chloride, 0.5 mM chenodeoxycholine, 35% ethylene glycol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97926 Å

Detector

Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 16, 2021 / Details: monochromator

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97926 Å / Relative weight: 1

Reflection

Resolution: 2.08→50 Å / Num. obs: 57573 / % possible obs: 94.5 % / Redundancy: 3.4 % / R_merge(I) obs: 0.087 / R_pim(I) all: 0.05 / R_rim(I) all: 0.101 / Χ²: 0.899 / Net I/σ(I): 6.3 / Num. measured all: 193410

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.08-2.12	1.7	0.272	2115	0.876	0.224	0.354	0.926	70.4
2.12-2.15	1.8	0.248	2424	0.888	0.193	0.316	0.935	81.5
2.15-2.2	1.9	0.257	2648	0.887	0.197	0.325	0.963	86.5
2.2-2.24	2.1	0.254	2746	0.923	0.189	0.319	0.93	92.1
2.24-2.29	2.3	0.287	2827	0.891	0.205	0.355	0.96	93.7
2.29-2.34	2.6	0.3	2888	0.883	0.207	0.367	0.932	95.3
2.34-2.4	2.8	0.265	2881	0.933	0.177	0.321	0.918	95.6
2.4-2.47	3.1	0.255	2883	0.931	0.165	0.306	0.917	94.7
2.47-2.54	3.5	0.248	2955	0.935	0.152	0.292	0.932	99.3
2.54-2.62	3.8	0.254	3030	0.947	0.151	0.297	0.931	98.2
2.62-2.71	3.9	0.241	2940	0.945	0.14	0.28	0.921	98.1
2.71-2.82	3.9	0.212	2986	0.954	0.122	0.246	0.926	98.8
2.82-2.95	3.8	0.186	2965	0.962	0.107	0.215	0.914	96.7
2.95-3.11	4.2	0.157	2991	0.978	0.087	0.18	0.877	98.6
3.11-3.3	4.4	0.118	2996	0.988	0.063	0.135	0.862	99
3.3-3.56	4.3	0.086	3044	0.993	0.046	0.098	0.883	98.5
3.56-3.91	4	0.068	2967	0.993	0.038	0.078	0.876	97.4
3.91-4.48	4.3	0.05	3074	0.996	0.027	0.058	0.911	99.4
4.48-5.64	4	0.044	3054	0.997	0.024	0.051	0.885	98.4
5.64-50	3.9	0.04	3159	0.998	0.022	0.046	0.786	97.5

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Processing

Software

Name	Version	Classification
HKL-3000		data scaling
PHENIX	1.19.2_4158	refinement
PDB_EXTRACT	3.27	data extraction
HKL-3000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5KEW

5kew

Resolution: 2.08→44.78 Å / SU ML: 0.2266 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.0728
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2236	2007	3.7 %
R_work	0.1882	52297	-
obs	0.1896	54304	88.87 %

Solvent computation

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

Displacement parameters

B_iso mean: 46.36 Å²

Refinement step

Cycle: LAST / Resolution: 2.08→44.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7365	0	200	261	7826

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0104	7735
X-RAY DIFFRACTION	f_angle_d	0.7753	10463
X-RAY DIFFRACTION	f_chiral_restr	0.0628	1156
X-RAY DIFFRACTION	f_plane_restr	0.0064	1303
X-RAY DIFFRACTION	f_dihedral_angle_d	13.8392	2882

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 (%)
2.08-2.13	0.2329	77	0.2271	2054	X-RAY DIFFRACTION	49.59
2.13-2.18	0.2387	107	0.2202	2737	X-RAY DIFFRACTION	65.32
2.18-2.25	0.271	122	0.2131	3098	X-RAY DIFFRACTION	75.25
2.25-2.32	0.2534	130	0.2134	3517	X-RAY DIFFRACTION	83.36
2.32-2.4	0.2488	146	0.2135	3701	X-RAY DIFFRACTION	90.37
2.4-2.5	0.2619	153	0.2079	3923	X-RAY DIFFRACTION	93.72
2.5-2.61	0.2659	162	0.2019	4112	X-RAY DIFFRACTION	98.12
2.61-2.75	0.2267	150	0.189	4107	X-RAY DIFFRACTION	97.82
2.75-2.92	0.2288	157	0.1889	4057	X-RAY DIFFRACTION	98
2.93-3.15	0.2442	163	0.1945	4154	X-RAY DIFFRACTION	98.29
3.15-3.47	0.2165	155	0.1768	4168	X-RAY DIFFRACTION	98.65
3.47-3.97	0.1926	159	0.1732	4126	X-RAY DIFFRACTION	97.79
3.97-5	0.1887	161	0.1516	4233	X-RAY DIFFRACTION	99.14
5-44.78	0.2298	165	0.2122	4310	X-RAY DIFFRACTION	97.54

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	5.49963795375	-0.364365989821	0.842912434331	1.84069970907	1.1181264938	4.19361776065	0.220073152715	-0.380055951004	0.0590820611134	0.400825011082	-0.0998349984585	-0.16738885654	-0.0692080287442	0.12745526339	-0.0428824852583	0.193842560053	-0.0158422615783	0.00960480201192	0.124006850952	0.0223208082349	0.119531026585	37.6621461517	-5.60466421695	37.4065071395
2	2.04930411337	-1.05227942885	1.0480572408	2.90922546156	-4.13473326378	6.02549618017	-0.180166144235	-0.125781955066	0.351118218733	0.609399721072	-0.222386869736	-0.820436738189	-0.569367589785	0.338797197293	0.371146746605	0.140025317806	-0.0271512257419	-0.050037126435	0.170492174869	-0.00372193496786	0.186787470291	44.9165015317	1.07190661241	34.0378027662
3	3.77042855044	-0.758614942858	-0.378746173387	5.68688548816	-0.380417879298	4.06814026497	-0.0287439626293	-0.0133207199374	-0.0765900594288	0.269869188452	0.0349226713128	0.0932298330003	0.0772776039475	0.0726599344601	-0.0127241069172	0.0731040592434	-0.0471037522462	-0.0288944755893	0.088887920797	-0.00194576601578	0.129218982914	36.3803918803	-3.26216575466	28.3154508501
4	2.89111926619	-3.05998918038	-0.952108776695	4.50944182514	1.08130433019	1.3798014714	-0.0021300069299	0.100180616961	0.268161582567	-0.222714181878	-0.00793258516032	-0.00310811932614	-0.0133503899187	-0.0949175462119	-0.0822637404495	0.144413414719	0.0185660737411	-0.0257458027785	0.0235311008411	0.0259428793723	0.406474432155	30.5420653332	-2.77446686838	22.367947398
5	4.47009761222	-0.991953539992	-0.437826578976	6.50064416662	-2.27206762174	4.13172492643	0.210569387647	0.0757934333899	-0.970311537355	-0.339987608705	-0.013117084486	-0.0736576793635	0.866069949724	0.322647252923	-0.446999185927	0.383793098836	0.112190514835	-0.227617377886	0.250205216379	0.00357998216076	0.804817422837	50.3696281963	-12.6652692152	25.2117259912
6	8.43276055956	0.473048925607	2.36350794422	5.53028203015	0.265955260855	6.14040254559	0.0416275067248	0.494604580215	0.0845907146767	-0.242991895686	0.176596979774	-0.0713763334281	-0.382891611185	0.442199017228	-0.170035535387	0.121981831497	0.000625897595745	0.00230875935813	0.0919128011957	0.0140952935396	0.210978417724	43.7278652562	-0.800478279838	22.5744556825
7	8.42494079097	0.740577186805	-2.95565250388	2.76225434394	-0.114474021447	2.95642055776	-0.0839606739952	-0.176983849867	0.0247219116354	-0.0154687853297	0.0753839423246	0.288189559653	0.054607274871	-0.21843551637	-0.0781579498573	0.127573225097	-0.00785324769543	-0.0471596914374	0.0892313956254	0.0249827869921	0.136174908647	21.3130990421	-12.2427539783	23.7690965354
8	6.76377936938	-0.642856684753	-1.40857940447	2.55690787859	0.279993172558	2.69738107178	-0.0626958701376	1.02074194606	0.229904851114	-0.417036175128	0.208676157713	-0.177440415637	0.0429853305766	-0.178526142798	0.0128582333353	0.195547444085	-0.015873938626	0.0133394998111	0.145363394046	-0.0379198945053	0.169716960858	28.8542000069	-15.9097693636	16.39296783
9	3.78668025996	0.317989718752	-0.910125112176	4.46170852982	0.422281121698	5.13111334591	0.26966059609	-0.195536556947	-0.0438528454414	0.244689446152	0.0917525857722	0.292140283957	-0.0872176937152	0.501067721798	-0.209916061533	0.111616434162	0.0020185240619	0.00391478799608	0.115312572878	-0.0193102206117	0.215990740091	23.7600131661	-22.0396260519	23.5629731827
10	2.59667801303	-2.29553941809	1.37115735918	3.02268624764	-3.81987536733	7.80937004536	0.0720141440655	0.689764680006	-0.0389706859444	0.0299114909607	-0.26629822111	0.0755613003352	-0.236979771363	0.119588007332	-0.110168555267	0.541514532582	0.0422603599501	-0.066131103283	0.362328654752	-0.0688593304028	0.291675288992	26.4615246214	-25.3858760388	7.11511583775
11	8.54710406281	-0.892700207975	-5.09355246984	0.149489113828	1.06387594845	8.08418801525	0.459224434846	0.402762992074	-0.431885047221	0.395276081074	-0.241052817819	-0.451244363447	-0.722675461544	0.362651069068	0.274408051813	0.382113313556	0.0149122594073	-0.00497907403185	0.223238786797	0.0858197550403	0.491060479151	29.9229049728	-30.2503266523	25.0309015183
12	2.74998379439	-0.150147961858	0.138868126975	5.53302218493	0.571951756291	5.01026209659	0.131885275947	-0.369453127373	-0.0774072576029	0.562713516681	0.0183027264103	0.331008220341	0.147171624791	-0.378445399998	0.118652274492	0.144946886944	-0.03314945505	0.00766518226893	0.0811563092292	0.0409137844708	0.212827401017	27.2093677431	-12.1447380222	31.4436297208
13	3.22453439335	-1.67559434767	0.299619312107	6.17698849378	-0.819361482009	4.643718808	0.155160240569	-0.0303520543753	0.00417243755429	-0.0428740741818	0.15186531327	0.864216987012	-0.399031213935	-0.539115356006	-0.10152921027	0.149950746971	-0.0173330260099	-0.00210732598298	-0.0834277092788	0.0626701852715	0.303894382408	23.9518066882	-8.27105332015	26.4252414383
14	5.8575754919	0.270280557451	0.673270796839	3.88245557755	-3.37866589018	6.51783365048	0.309452700921	0.908951374775	1.06093006167	-0.239237406281	-0.204262289946	0.578566474809	-1.08220354637	-0.73134188446	-0.383841154898	0.239851006877	0.0436613517317	0.0338737454336	0.247488311531	0.0627426003649	0.305648970047	-5.24926578558	-9.00726698413	5.40203057413
15	4.08962585078	-0.935172019988	0.196037195892	3.15945230737	-2.23851693988	4.16105396732	0.0741923193704	0.497087604607	-0.0841957783985	-0.153471936999	-0.0511581807927	-0.231024784127	0.133563743936	0.238434251864	0.0110072946283	0.120575777249	0.0132141424983	-0.0227319004371	0.204105754239	-0.0515115770995	0.16125944052	8.74104170555	-20.0147767141	7.23604152361
16	4.62465682791	-0.492489751021	0.157048199028	4.91265008839	-2.43627421658	4.71513424635	0.102344217815	0.34976647424	-0.401561684333	0.0564855813853	-0.128666922409	0.240852044518	0.264074825712	0.0890339718601	-0.143220509921	0.0923829806267	0.000417170913464	-0.00506794225974	0.171217665838	-0.0496796086053	0.136845119558	3.76986778533	-23.6749537775	13.1365735935
17	5.93358093041	0.54991805626	-0.450966990782	6.52756225208	0.339447817951	5.53924257615	0.137939575132	0.113631896004	-0.350897946198	0.381370571291	0.0622707134855	0.0857551338641	0.0886256007344	0.237939534746	-0.0451158658581	0.109541432086	0.0274407135269	0.00575296135109	0.183797970829	-0.023917086869	0.18347588634	-0.0200206461499	-22.0462860279	16.5964946458
18	5.83235559264	1.54950272787	-0.543188920037	2.96987850401	1.08805866414	4.35557604292	0.110958634649	-0.135734503429	0.265744841274	0.133512903107	0.0995527254472	-0.205107394074	-0.183939453591	0.323902656438	-0.0449596703928	0.106343952413	-0.0272530320043	0.00957302286359	0.130911082176	0.012232428605	0.238090041412	7.87217381027	-16.1915407626	20.0483150211
19	5.89632550751	4.8455276872	1.97448378662	5.01620437978	1.50946764107	2.2190695967	-0.326531459513	0.395866427074	-0.0365411684069	-0.228458603029	0.277335843585	0.0820700077094	0.0198706390735	0.0128029595848	0.101493449461	0.106117865966	0.00933759043893	0.034450528303	0.117528621931	0.00982520823618	0.125695374212	-14.667270256	-21.6300181968	18.9835428191
20	6.28519983741	2.54970375262	1.19897164967	3.33956708181	0.918773241012	3.96205548681	0.0938171568329	-0.879868176864	0.533392169998	0.3141897329	-0.148663047045	-0.0321731724994	-0.163641765141	-0.0413613488945	0.054616492846	0.171662147392	0.0298178220876	0.0216451902356	0.154646927046	-0.0501249337523	0.248483867162	-10.1184980148	-14.5360252063	26.481005416
21	3.0847287152	-0.657589844644	-1.53745082196	2.26959874933	1.72286521142	2.4375327342	0.102880637651	0.0651035900119	0.388390100798	0.162656806889	0.018092782416	0.195196134777	-0.0150832545001	-0.27698330238	-0.0681211342076	0.192842748669	-0.0298146585753	0.0100746564199	0.0913314941673	0.0394759896934	0.292286920675	-17.7600457332	-11.7519784713	19.1912052788
22	3.17206978384	-0.962917534201	-3.08128816644	0.87316695788	1.94382249242	7.19101227229	0.168158221438	-0.242690971621	0.732171519171	0.152955358222	0.226516014602	-0.0948134012133	-0.546372374722	0.241104134381	-0.21815986307	0.312330149121	-0.0272151064573	-0.0406911922504	0.256728738006	0.019125766854	0.492418020604	-15.0926682075	-8.91670025745	22.3373547114
23	4.94512922146	-0.963767984276	-0.465982800385	3.17809466161	-0.537750513688	5.55826324355	-0.0125894827034	0.135307338651	-0.146044349323	0.0844880706205	0.0958414786283	0.210948623043	0.293320105418	-0.232141699419	-0.0607320979329	0.0525427494367	-0.0120708683214	-0.0230038230814	0.123399186342	0.0165004103698	0.177358382036	-9.62863085616	-20.4775624311	14.6395278862
24	4.81185791513	1.7815914808	0.226689126814	2.6903659128	-1.72348650701	4.94914538924	0.301137242219	0.578082422838	0.0673179745043	-0.435078185818	-0.343490420309	0.301766871863	-0.431638241009	-0.819562279286	0.0296347853031	0.433836820453	0.169576775672	0.0740247011886	0.348806173262	-0.0309278069332	0.208139753659	29.2824435823	-7.21321704472	47.4674225774
25	4.03750545446	-2.97062616935	-2.15757849913	2.72697055582	1.30812732586	2.04885923549	0.104940641714	0.0965198343864	0.411123541723	-0.468179035818	-0.258978962052	0.294312370563	-0.98618791985	-0.851442090569	0.496325672727	0.838857884525	0.551146210151	0.128031980044	0.553560603643	-0.00031202805206	0.362569774311	25.6031144552	3.19540982322	51.2365866251
26	3.31725349612	5.03974264093	1.62401854443	8.5815884131	2.2190047098	6.69522986862	0.0308269537933	-0.405286350062	-0.416048149575	-0.353488828794	-0.0423394714957	-0.462264747888	-0.0799494411241	0.0340078609002	0.0612988704658	0.312652139883	0.15722399448	0.0418725673558	0.30283259353	0.0723392756358	0.249164236252	33.6606157333	-4.35498070331	55.9339770528
27	9.27338929848	-0.591251740731	0.944657138053	3.87729697138	-0.259491497977	3.96834448822	0.105642688892	-0.748555305786	0.127460668549	0.00442935982489	-0.0170323727316	0.378249113446	-0.378200082575	-0.53513483698	-0.0555699738523	0.321338295468	0.183131490722	0.0400208260594	0.526141703524	-0.00327772934767	0.215382427596	24.9543234681	-2.62319098753	61.6904688796
28	6.29326850092	-2.43101024709	-0.67414649686	2.57758063128	0.684312041484	1.41103835534	-0.390726506715	-0.55960951086	-0.013884123032	0.122248950067	0.231616940669	-0.0983877121545	0.338916734285	0.947387045198	0.227463713827	0.446989643567	0.273722454438	0.043707026479	0.915731576909	0.103010770836	0.222047703781	45.437232841	-10.3439901422	61.7117328044
29	3.72448317211	-2.24008006673	0.711543899882	3.05966907739	0.260932207607	1.67829392894	-0.838444976981	-0.788447472256	-0.285668387635	0.723490944607	0.345158009666	0.362410981401	0.360763833327	0.169932941697	0.181303882971	0.589471559952	0.312433581244	0.0983752086519	0.946357547513	0.212065755187	0.405137472889	40.5924200642	-13.5866388693	68.013323168
30	6.8255730136	-4.34723198053	-0.912371662719	2.78473123	0.584549994378	0.122958592053	0.823282546981	1.53852465019	0.15506308947	-0.9288108612	-1.27323086972	0.126623453114	0.412387023675	0.550593100284	0.240844148237	0.904406666419	0.314202423855	0.0579788906449	1.51899110837	0.052091174345	0.778656249779	32.4202585973	-8.03824826752	81.7066996879
31	0.847958592025	0.457413883201	0.0754000997965	1.20941276651	-0.777453875865	1.80985740957	0.000912769294075	-0.678083527049	-0.412982976935	0.0230013372866	0.0312521189871	-0.240952508982	0.524573205048	0.0606320642479	0.288735002093	0.730512296991	0.437890193093	0.123727223413	0.888343382634	0.296335262759	0.489995884262	44.8515844156	-21.9230334066	61.4987197189
32	3.0080713341	0.0843903302854	3.46146853754	2.27747886016	-0.730304993702	9.23432991351	-0.291804159776	-1.22653316268	-0.314512975171	0.155562667761	-0.39297627465	-0.291486057514	0.664826676194	0.225154956853	-0.0250603008466	0.895687826894	0.245039492267	0.166095997751	1.52537232541	0.42905579854	0.672772916966	42.8182425997	-19.8707734139	80.2392275683
33	1.59895230597	0.891033205077	0.633238492785	6.25389635828	-2.18973258239	1.37373225224	-0.244866742735	-1.07827371594	-0.965363716048	-0.0995692605122	0.0660890898343	0.00527008541551	1.25311411306	0.0516556418194	-0.0996007253451	1.09963355629	0.240084601812	0.192276971806	0.654412887437	0.310184015687	0.776528411858	37.9521492495	-27.9515910064	63.0917694034
34	3.72929645209	0.991148466015	-0.873375040373	8.10593950204	-2.45750377529	6.59675027041	-0.0547246857731	-0.559133076033	-0.21771190537	-0.0981731840043	0.0502953292889	-0.259874405743	0.250244482013	0.276147121088	0.109668635857	0.311893699285	0.161013825258	0.0163692661481	0.307242740805	0.0858381914482	0.219254256493	41.2976653792	-10.7719122151	54.7294974824
35	2.02374684266	-0.0771979209397	-1.74724131767	2.63580521812	1.05487878457	3.88784928607	0.128115741133	-0.937336563794	0.0936867214854	-0.286553214522	-0.290244040477	-0.209768683372	0.319613068478	0.125864973805	0.295024316395	0.651715164866	0.443999561853	0.0676684407277	1.48598971133	0.013890577877	0.465557570093	-4.51973493868	8.63632755245	78.9639700224
36	2.63750696306	-0.313890871018	-2.14725347252	1.41502134573	1.00370709901	2.91033022405	-0.181538056677	-0.430360522841	-0.0357271257662	0.220786088588	-0.0630849285593	0.196909356206	-0.0585384487955	-0.392922022351	-0.360707232589	0.506937918153	0.458227090525	0.238605281742	1.402468646	0.165072811373	0.377111775043	-14.7907072787	4.91498275273	75.7858743421
37	2.14770023064	0.788916267841	-0.860603684101	3.21710248029	-0.577044521172	3.80467835571	-0.175883617426	-0.567988427526	0.0250967521829	0.686158809927	0.256396131554	0.143630997853	-0.229889867413	-0.312153778145	-0.0770079487663	0.710620887381	0.471526500356	0.12334336282	0.999788877997	0.0972808424346	0.263864792494	-5.56303866051	3.72058355276	72.3070819613
38	6.79208730493	-0.148579079327	-2.08608795714	3.19222107771	1.64425301887	3.21311592642	0.156479762702	-0.151509870653	0.481085983292	0.101950424663	0.163275335241	0.112358172102	-0.226901730848	-0.185743756582	-0.306198748206	0.436475456906	0.349091791137	0.0651443309769	0.687871384334	0.0901921710502	0.270734342634	-3.57253848548	4.5656355172	68.3292227358
39	7.46832732509	-0.134981816548	0.268075911759	9.15576171237	-0.636192018535	1.96827439588	-0.0814014800028	-0.227026985781	-0.98478632936	-0.552908735296	0.211139422224	0.61399867391	0.695448945234	-0.323159963097	-0.100820640166	0.948517673506	0.220750510869	-0.0968993278137	0.823032553995	0.359119280758	0.896515083985	0.113578048945	-9.97881848106	70.1345108667
40	7.8086936778	-3.10186109289	1.51369059975	4.4969303439	-0.946591824894	2.06224929934	0.0301433909578	0.0528924370866	0.358761281189	0.106791360758	0.232327153177	0.166377698325	-0.267497520472	-0.311950707049	0.0017348552694	0.471402969401	0.390756547664	-0.000998908033491	0.888143485996	0.0851102672879	0.390887239734	-2.97413554005	4.77892072074	63.273619362
41	5.79328524677	-2.46878054119	-1.45008595512	1.12214922083	0.841001883192	1.36717042958	0.320228311232	0.509220732238	1.19789279776	-0.439396526142	-0.234043668254	-0.766125206923	-0.253203008977	0.255940264487	-0.36174522001	0.803781793628	0.429701497812	0.441014806006	1.09399597774	0.0672309158006	1.1790860468	-12.9025031467	18.0020706888	64.9541124695
42	1.33102618272	-0.496020294328	0.562372124367	0.970234696778	0.742238412813	2.49275432919	-0.123052483848	0.0396607192809	-0.0480658863511	0.374372037725	0.10759360458	0.0832210134893	0.21321350637	-0.315377284401	0.0100611017572	0.490637066795	0.333438593616	0.0529587269647	1.23145549627	0.252995497346	0.280327893125	-13.5476007124	3.53151769598	65.4605135707
43	5.09162341561	-1.34663757005	0.722773066408	1.94563951306	-0.122875441902	1.96297757232	0.015400984314	0.110724036201	-0.206242277245	-0.162691765252	0.207774271586	0.185195018627	-0.306045323785	-0.117351414425	-0.134828895812	0.464814792926	0.217086848659	0.0352899832576	0.680468544282	0.0960201154778	0.201452956205	7.27379593225	5.02745650878	61.1781251286
44	6.67865853927	-0.740955161784	-0.557280965466	3.19433104773	0.00540056040192	1.00484181879	0.11236689906	-0.2576263989	0.814806444105	-0.255135609892	-0.142255477778	0.0240100489801	-0.181800102429	-0.299634890467	0.0436870952725	0.514608931002	0.187291644288	0.0883158683935	0.667023024767	0.0979234835103	0.46379155095	12.913919508	9.9373443722	60.7262486864
45	5.14288834322	-1.71241941336	-0.61551072362	2.98274341066	-0.907355603845	4.68205658033	0.232013377158	-0.0225350422828	0.991257374541	-0.0272244296402	0.591799737773	0.201513167056	-0.298413667818	0.679883246705	-0.650927427747	0.75013636235	0.0420094129022	0.169550731218	0.697296228515	0.047688829249	0.902826706848	13.5976760494	15.7032014663	55.4256794258
46	4.04011569404	0.653863602577	-0.175642127985	3.98120216777	-0.318744481315	4.38796006962	-0.0428534136878	-0.9326014413	0.0341028650148	0.88087754566	0.429984497184	-0.539233637738	-0.230302981485	0.169315791021	-0.256953561009	0.497045501378	0.328217386406	-0.0100075539923	0.962285959052	0.00737186987747	0.369978278831	7.00893110819	4.20914093997	71.335584021

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 165 through 182 )	A	A	165 - 182	1 - 18
2	2	chain 'A' and (resid 183 through 199 )	A	A	183 - 199	19 - 35
3	3	chain 'A' and (resid 200 through 221 )	A	A	200 - 221	36 - 57
4	4	chain 'A' and (resid 222 through 233 )	A	A	222 - 233	58 - 69
5	5	chain 'A' and (resid 234 through 239 )	A	A	234 - 239	70 - 75
6	6	chain 'A' and (resid 240 through 253 )	A	A	240 - 253	76 - 89
7	7	chain 'B' and (resid 29 through 42 )	B	C	29 - 42	1 - 14
8	8	chain 'B' and (resid 43 through 76 )	B	C	43 - 76	15 - 48
9	9	chain 'B' and (resid 77 through 109 )	B	C	77 - 109	49 - 81
10	10	chain 'B' and (resid 110 through 121 )	B	C	110 - 121	82 - 93
11	11	chain 'B' and (resid 122 through 131 )	B	C	122 - 131	94 - 103
12	12	chain 'B' and (resid 132 through 153 )	B	C	132 - 153	104 - 125
13	13	chain 'B' and (resid 154 through 161 )	B	C	154 - 161	126 - 133
14	14	chain 'C' and (resid 164 through 168 )	C	J	164 - 168	1 - 5
15	15	chain 'C' and (resid 169 through 199 )	C	J	169 - 199	6 - 36
16	16	chain 'C' and (resid 200 through 212 )	C	J	200 - 212	37 - 49
17	17	chain 'C' and (resid 213 through 226 )	C	J	213 - 226	50 - 63
18	18	chain 'C' and (resid 227 through 253 )	C	J	227 - 253	64 - 90
19	19	chain 'D' and (resid 29 through 42 )	D	L	29 - 42	1 - 14
20	20	chain 'D' and (resid 43 through 76 )	D	L	43 - 76	15 - 48
21	21	chain 'D' and (resid 77 through 109 )	D	L	77 - 109	49 - 81
22	22	chain 'D' and (resid 110 through 139 )	D	L	110 - 139	82 - 111
23	23	chain 'D' and (resid 140 through 161 )	D	L	140 - 161	112 - 133
24	24	chain 'E' and (resid 165 through 182 )	E	R	165 - 182	1 - 18
25	25	chain 'E' and (resid 183 through 205 )	E	R	183 - 205	19 - 41
26	26	chain 'E' and (resid 206 through 226 )	E	R	206 - 226	42 - 62
27	27	chain 'E' and (resid 227 through 253 )	E	R	227 - 253	63 - 89
28	28	chain 'F' and (resid 30 through 42 )	F	S	30 - 42	1 - 13
29	29	chain 'F' and (resid 43 through 73 )	F	S	43 - 73	14 - 44
30	30	chain 'F' and (resid 74 through 79 )	F	S	74 - 79	45 - 50
31	31	chain 'F' and (resid 80 through 109 )	F	S	80 - 109	51 - 80
32	32	chain 'F' and (resid 110 through 121 )	F	S	110 - 121	81 - 92
33	33	chain 'F' and (resid 122 through 132 )	F	S	122 - 132	93 - 103
34	34	chain 'F' and (resid 133 through 161 )	F	S	133 - 161	104 - 132
35	35	chain 'G' and (resid 165 through 182 )	G	W	165 - 182	1 - 18
36	36	chain 'G' and (resid 183 through 200 )	G	W	183 - 200	19 - 36
37	37	chain 'G' and (resid 201 through 214 )	G	W	201 - 214	37 - 50
38	38	chain 'G' and (resid 215 through 221 )	G	W	215 - 221	51 - 57
39	39	chain 'G' and (resid 222 through 226 )	G	W	222 - 226	58 - 62
40	40	chain 'G' and (resid 227 through 233 )	G	W	227 - 233	63 - 69
41	41	chain 'G' and (resid 234 through 239 )	G	W	234 - 239	70 - 75
42	42	chain 'G' and (resid 240 through 253 )	G	W	240 - 253	76 - 89
43	43	chain 'H' and (resid 30 through 59 )	H	X	30 - 59	1 - 30
44	44	chain 'H' and (resid 60 through 109 )	H	X	60 - 109	31 - 80
45	45	chain 'H' and (resid 110 through 134 )	H	X	110 - 134	81 - 105
46	46	chain 'H' and (resid 135 through 161 )	H	X	135 - 161	106 - 132

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-Protein , 2 types, 8 molecules ACEGBDFH

-Non-polymers , 5 types, 280 molecules

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Movie

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Structure viewers

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Viewer log

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This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 2 types, 8 molecules ACEGBDFH

-
Non-polymers , 5 types, 280 molecules

-
Details

-
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

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Yorodumi