PDB-7m7a: Legionella pneumophila MavQ lipid kinase

ID or keywords:

Entry

Database: PDB / ID: 7m7a

Title

Legionella pneumophila MavQ lipid kinase

Components

Phosphoinositide 3-kinase MavQ

Keywords

TRANSFERASE

Function / homology

ADENOSINE-5'-DIPHOSPHATE / Uncharacterized protein

Function and homology information

Biological species

Legionella pneumophila subsp. pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.2 Å

Authors

Tomchick, D.R. / Tagliabracci, V.S. / Hsieh, T.S. / Lopez, V.A.

Funding support

United States,

Poland, 10items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	DP2GM137419	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01GM113079	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	T32GM008203-29	United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	F30HL143859-01	United States
National Institutes of Health/Office of the Director	S10OD025018	United States
Robert A. Welch Foundation	I-1911	United States
Robert A. Welch Foundation	I-1789	United States
Cancer Prevention and Research Institute of Texas (CPRIT)	RP170674	United States
National Center for Research and Development (Poland)	PPN/BEK/2018/1/00431	Poland
National Institutes of Health/Office of the Director	S10OD021685	United States

Citation

Journal: Science / Year: 2021
Title: Dynamic remodeling of host membranes by self-organizing bacterial effectors.
Authors: Hsieh, T.S. / Lopez, V.A. / Black, M.H. / Osinski, A. / Pawlowski, K. / Tomchick, D.R. / Liou, J. / Tagliabracci, V.S.

History

Deposition	Mar 27, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 28, 2021	Provider: repository / Type: Initial release
Revision 1.1	May 12, 2021	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Jun 9, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	May 22, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7m7a.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb7m7a.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	7m7a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7m7a_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	7m7a_full_validation.pdf.gz	1.5 MB	Display
Data in XML	7m7a_validation.xml.gz	71.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m7/7m7a ftp://data.pdbj.org/pub/pdb/validation_reports/m7/7m7a	HTTPS FTP

-
Related structure data

Similar structure data	22829 2v5p-1 4z54-d 6r9p-d 4uw2-2 6j11-1 5wu6-3 4jo7-d 6r9m-d 1jp7-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phosphoinositide 3-kinase MavQ

B: Phosphoinositide 3-kinase MavQ

C: Phosphoinositide 3-kinase MavQ

D: Phosphoinositide 3-kinase MavQ

hetero molecules

276 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phosphoinositide 3-kinase MavQ

hetero molecules

defined by author&software
Evidence: gel filtration
68.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphoinositide 3-kinase MavQ

hetero molecules

defined by author&software
68.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Phosphoinositide 3-kinase MavQ

hetero molecules

defined by author&software
68.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Phosphoinositide 3-kinase MavQ

hetero molecules

defined by author&software
68.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.399, 210.235, 499.861
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 2 through 15 or resid 29...
d_2	ens_1	(chain "B" and (resid 2 through 576 or resid 701 through 702))
d_3	ens_1	(chain "C" and (resid 2 through 15 or resid 29...
d_4	ens_1	(chain "D" and (resid 2 through 48 or resid 54...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	GLY	PHE	A	1 - 14
d_1	2	ens_1	THR	LEU	A	20 - 39
d_1	3	ens_1	TYR	MET	A	45 - 163
d_1	4	ens_1	VAL	GLN	A	166 - 195
d_1	5	ens_1	TYR	VAL	A	198 - 390
d_1	6	ens_1	HIS	THR	A	394 - 537
d_1	7	ens_1	ADP	ADP	B
d_2	1	ens_1	GLY	THR	D	1 - 520
d_2	2	ens_1	ADP	ADP	E
d_3	1	ens_1	GLY	PHE	G	1 - 14
d_3	2	ens_1	THR	LEU	G	17 - 36
d_3	3	ens_1	TYR	MET	G	42 - 160
d_3	4	ens_1	VAL	GLN	G	164 - 193
d_3	5	ens_1	TYR	VAL	G	195 - 387
d_3	6	ens_1	HIS	THR	G	391 - 534
d_3	7	ens_1	ADP	ADP	H
d_4	1	ens_1	GLY	LEU	J	1 - 34
d_4	2	ens_1	TYR	MET	J	37 - 155
d_4	3	ens_1	VAL	GLN	J	159 - 188
d_4	4	ens_1	TYR	VAL	J	190 - 382
d_4	5	ens_1	HIS	THR	J	386 - 529
d_4	6	ens_1	ADP	ADP	K

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.0439845537993, -0.98605493317, 0.16050242303), (-0.98491040732, -0.0697168814005, -0.158401534082), (0.167382342494, -0.151113286045, -0.974242231789)	27.2102100037, 50.2256193289, 126.774710276
2	given	(0.965705040742, 0.0369804120381, 0.25699459802), (-0.0453210221846, 0.998618125506, 0.0266053445399), (-0.255655587137, -0.037340173211, 0.966046547652)	-33.0950466373, 49.5104241072, 4.88953427156
3	given	(-0.00305634303733, -0.98961271635, -0.143726582112), (-0.979056562149, 0.0322193229313, -0.201022793095), (0.203565485486, 0.140102058758, -0.968985297231)	31.1065770769, 100.838476981, 116.581977761

#1: Protein	Phosphoinositide 3-kinase MavQ Mass: 68479.328 Da / Num. of mol.: 4 / Fragment: MavQ, UNP residues 1-580 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2975 / Plasmid: ppSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta References: UniProt: Q5ZRA8, phosphatidylinositol-3-phosphatase
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Sequence details	SEFELRRQAS is from the purification tag

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.33 Å³/Da / Density % sol: 63.07 % / Mosaicity: 0.359 °
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% (w/v) PEG 3350, 0.05 M sodium chloride, 0.1 M Hepes, 5 mM magnesium chloride, 5 mM AMP-PNP, 35% ethylene glycol

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97951 Å

Detector

Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 11, 2018 / Details: monochromator

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97951 Å / Relative weight: 1

Reflection

Resolution: 3.2→50 Å / Num. obs: 60636 / % possible obs: 98.8 % / Redundancy: 30.4 % / R_merge(I) obs: 0.168 / R_pim(I) all: 0.029 / R_rim(I) all: 0.171 / Χ²: 1.072 / Net I/σ(I): 4.5 / Num. measured all: 1844250

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
3.2-3.26	13.8	1.003	2738	0.744	0.244	1.04	1.056	90.5
3.26-3.31	15.5	0.974	2889	0.754	0.225	1.005	1.047	94.6
3.31-3.38	18	0.906	2902	0.906	0.199	0.931	1.042	97
3.38-3.45	19.9	0.832	2983	0.922	0.173	0.852	1.068	97.1
3.45-3.52	22.7	0.796	2938	0.947	0.159	0.813	1.067	98.4
3.52-3.6	24.8	0.641	2985	0.983	0.123	0.654	1.064	98.6
3.6-3.69	26.6	0.603	3052	0.986	0.113	0.614	1.107	99.5
3.69-3.79	28.5	0.526	3011	0.991	0.096	0.535	1.103	100
3.79-3.91	29.6	0.412	3054	0.995	0.074	0.419	1.14	100
3.91-4.03	29	0.384	2999	0.995	0.069	0.391	1.143	100
4.03-4.18	33.7	0.349	3041	0.996	0.06	0.354	1.145	100
4.18-4.34	35	0.303	3115	0.997	0.051	0.307	1.181	100
4.34-4.54	37	0.263	2999	0.998	0.044	0.266	1.186	100
4.54-4.78	38.1	0.218	3088	0.998	0.036	0.221	1.194	100
4.78-5.08	38.5	0.2	3066	0.999	0.032	0.202	1.175	100
5.08-5.47	36.5	0.201	3078	0.999	0.033	0.204	1.136	100
5.47-6.02	41.5	0.195	3089	0.998	0.031	0.197	1.082	100
6.02-6.89	40.3	0.167	3141	0.998	0.027	0.169	1.029	100
6.89-8.67	37	0.108	3161	0.999	0.018	0.109	0.92	99.8
8.67-50	37	0.07	3307	0.999	0.012	0.071	0.614	100

-
Processing

Software

Name	Version	Classification
PHENIX	1.19.2-4158	refinement
HKL-3000		data scaling
HKL-3000		data reduction
PDB_EXTRACT	3.27	data extraction
SHELXD		phasing
MLPHARE		phasing
PARROT		phasing
BUCCANEER		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 3.2→49.31 Å / SU ML: 0.3784 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4635
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2834	1995	4.03 %
R_work	0.2395	47478	-
obs	0.2412	49473	80.86 %

Solvent computation

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

Displacement parameters

B_iso mean: 58.58 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→49.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17540	0	112	0	17652

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0023	18082
X-RAY DIFFRACTION	f_angle_d	0.5778	24497
X-RAY DIFFRACTION	f_chiral_restr	0.0368	2659
X-RAY DIFFRACTION	f_plane_restr	0.0039	3130
X-RAY DIFFRACTION	f_dihedral_angle_d	13.5782	6706

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	1.02404002821
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.999764838008
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	1.01253664508

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 (%)
3.2-3.28	0.3453	56	0.327	1322	X-RAY DIFFRACTION	31.93
3.28-3.37	0.4103	66	0.3269	1572	X-RAY DIFFRACTION	38.13
3.37-3.47	0.3877	77	0.3073	1827	X-RAY DIFFRACTION	44.02
3.47-3.58	0.3653	96	0.2878	2312	X-RAY DIFFRACTION	56.04
3.58-3.71	0.2976	129	0.281	3052	X-RAY DIFFRACTION	73.41
3.71-3.86	0.3296	154	0.2589	3676	X-RAY DIFFRACTION	88.7
3.86-4.03	0.2977	172	0.2437	4083	X-RAY DIFFRACTION	98.59
4.03-4.24	0.2631	176	0.2305	4175	X-RAY DIFFRACTION	99.91
4.24-4.51	0.2554	174	0.2044	4162	X-RAY DIFFRACTION	99.91
4.51-4.86	0.2519	176	0.1946	4184	X-RAY DIFFRACTION	99.93
4.86-5.35	0.2615	178	0.2098	4234	X-RAY DIFFRACTION	99.95
5.35-6.12	0.289	177	0.2557	4223	X-RAY DIFFRACTION	100
6.12-7.7	0.3413	179	0.261	4266	X-RAY DIFFRACTION	99.84
7.7-49.31	0.2276	185	0.2266	4390	X-RAY DIFFRACTION	98.39

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	0.726686109725	0.429640997709	-0.748071005937	1.26978575783	-0.376768313828	1.66858505737	-0.0427324370593	-0.372095039914	-0.179547510077	0.501331838416	-0.051668532921	-0.199138595635	0.217918403908	0.136629805163	0.0555943095512	0.732161085493	-0.0268165296917	-0.0314455654374	0.692783911037	-0.043943842432	0.229993484394	11.9412798821	18.8537123162	118.597672806
2	0.936405128757	0.00509093715466	-0.327300888471	0.567433405112	-0.185883486487	1.23131688135	-0.00318724543657	-0.22507093775	-0.256383148054	0.265339377211	0.0135935514548	-0.341715653123	0.463631977723	0.653781465377	-0.0149627034932	0.464436125891	0.117677001342	-0.0354856921276	0.623360427004	-0.0330407190228	0.275985025693	23.3764326952	14.9605811062	103.586551308
3	0.0901117752595	-0.267258238215	-0.0759002827132	0.925092540943	-0.13573527242	1.18498136762	-0.0647267993703	-0.383999016595	0.245958802695	0.426905684364	0.144134320109	-0.196323198983	-0.373121458591	0.402950721859	-0.149800863206	0.413869426256	-0.128712056531	0.0890811561986	0.576094555146	-0.232363659104	0.270104526001	16.8695933416	35.3482064029	110.00665153
4	0.648860600204	0.316245659528	-0.269074023763	0.906524871629	-0.438668567107	0.449140215115	0.0596308310219	-0.0437899628162	0.0111162503306	0.0637311325866	0.1018658291	0.0153186024026	-0.00783343608003	0.135255554292	0.0706197335386	0.159672102263	-0.227958260451	0.0805213060311	0.269805674099	-0.061059177094	0.136149248221	12.7890440257	27.7341992195	83.900149321
5	0.986020387446	0.654867039941	-0.00820649804907	0.991180642543	0.000791260502214	0.0259063898661	-0.051163628221	0.164112479629	0.0420130156115	-0.191735973874	0.16855315604	-0.0960537806383	-0.0457808485997	0.0912185561293	0.0150834533909	0.336997138896	-0.316274874739	0.0258410433825	0.513017300251	-0.203360759931	0.394257948499	23.1952514933	50.5622904422	72.4139425767
6	0.633216711403	0.313497469954	-0.310649763062	0.547018284232	-0.226505945659	0.393833788851	0.0521132142709	-0.0226801687208	0.0161876764255	-0.0670724687867	0.0842219168609	0.0477180337783	-0.00432620054508	-0.00966431748448	0.0295961923181	0.23723560807	-0.375741536119	0.0596767942692	0.305453355054	-0.0121732698618	0.110081569431	11.8175637759	36.5460140181	68.5352424293
7	0.713955319791	-0.0219688443197	-0.471462403444	0.771571958096	1.00579292254	1.58647434061	-0.00294644486611	0.362682589878	-0.105364075718	-0.0550886533892	-0.00440714955806	-0.0161673950256	0.0580929927549	0.094535235342	-0.0224475612335	1.24454106091	-0.126058489611	0.0136062935246	0.702081570648	-0.12843137906	0.283016024048	28.462407703	19.2738648923	11.3587666913
8	1.52905325303	-0.764134755779	-0.326735331206	0.560654142296	-0.328662796248	1.40572251536	-0.201559158	0.416638884911	-0.581583279595	-0.153571393281	0.00889414272841	-0.158988531551	0.422165399095	0.0701597348974	0.0843722267982	1.10447009326	-0.0730169040542	0.11714834595	0.430609786993	-0.0593412774584	0.481192739853	31.9775539409	9.48032192407	27.2814128667
9	1.0308519784	-0.0294678460768	0.0371395458509	0.17595254031	0.113316602051	0.449102735544	-0.0792835402265	0.368914952331	-0.373022869932	-0.46274892688	0.0317244232458	-0.0414276489394	0.626832248015	-0.152226412264	-0.0657153423435	1.06035922089	-0.357565881186	-0.068306531053	0.389506381154	0.010254573646	0.262034563162	19.1921038015	14.7667602287	28.9452674892
10	1.08979473572	0.782437536196	-0.229055214075	1.03876414199	-0.103383055252	0.105567392852	0.0443508856713	-0.0793723805825	-0.064605382179	-0.0580821129938	-0.01597381588	0.276341294015	0.149020225343	-0.231751857352	0.070064079826	0.601099720552	-0.541129708522	-0.163297789998	0.506959915089	0.0620773770444	0.34023710119	-3.27660405972	16.2161747545	50.4798165122
11	1.05292019341	0.540679431624	-0.0514553149516	1.10795907302	-0.119065138293	1.64487607201	0.00432341775633	0.0721623547328	0.147188979917	-0.0720905036401	0.106051241214	0.152795028026	0.0676476270211	-0.209977536403	-0.105806063353	0.363120085317	-0.358511140433	-0.0422242217854	0.413031293408	0.0979609406147	0.342193725009	-2.89058118445	26.3497827063	54.6020840114
12	1.31522224299	0.828738401815	-0.595812146437	0.853680871153	-0.420615489239	0.571819523009	0.124780302564	-0.195494970992	-0.178921697718	0.137813808427	-0.0525824306801	-0.0662508373562	0.0295507699229	0.0307239591781	0.0084377140461	0.334454226972	-0.33821599544	-0.0976918454259	0.308703419271	0.0137203750923	0.219954657863	10.7307807818	23.576891135	59.3704729291
13	0.710029641108	-0.226396982914	-0.414579288288	0.30828795339	0.142078674665	0.600538744097	-0.189615111671	-0.199145627018	-0.147825885853	0.366412021612	-0.00480974149605	-0.0700830220683	0.271757904064	0.239365411738	0.112767951206	1.15212510463	0.0565122327982	-0.00628477113336	0.473824419754	-0.0343881160588	0.275641292143	10.8083081735	68.2495626764	113.819922469
14	1.13665025652	-0.550427494574	-0.2161767921	4.26859115327	-1.44876826686	0.64399231604	-0.029978588567	-0.100735933076	-0.237207998363	0.38952668694	-0.0703963891637	-0.312905989278	0.265214178467	0.195500367486	0.0577861969304	0.867154398252	0.238935330112	-0.0255120437847	0.497462519596	-0.0242727527003	0.251467395542	14.8245926881	61.8205093595	96.0375305923
15	0.445592621256	-0.219114921053	0.174485142633	0.766616861836	0.564980668903	1.08242717943	0.062633544768	-0.280686223287	-0.13864728699	0.258299781505	0.0482739256633	-0.381249506286	0.0978915028159	0.376781815641	-0.0807749526761	0.565924918874	0.104480657376	-0.128810174702	0.540242546198	0.0918250558071	0.384176852766	20.4721199751	73.4243637702	96.8574739212
16	0.57418770529	0.181573969767	-0.43240224555	0.629661939406	-0.0435215659307	0.730267271046	-0.0741615040741	-0.124567538502	0.218032820255	0.302126004827	-0.0832918543067	-0.140251466428	0.0768449530905	0.289517522657	0.078480403414	0.385521567627	-0.326295289968	-0.0409242048266	0.261872746386	0.102522409124	0.23750791802	8.42559475543	79.2325195752	92.2368126929
17	0.190741003037	0.143297758661	-0.239274124645	0.675602240206	-0.728636307436	0.830764004996	-0.154795989535	0.313395995265	0.36536992375	-0.16601796487	0.119498407461	0.133283934937	-0.194279377878	0.0301846685912	0.056921493163	0.522359066533	-0.341746992483	-0.240004237451	0.516040620416	0.16213554801	0.679822787935	9.94839737982	100.94466337	66.0467037778
18	0.545701884837	0.136378008656	-0.0777899739488	0.318226630876	-0.00446999657417	0.284421062362	-0.0891125622436	0.0432163241304	0.100169375716	-0.0182095326769	-0.099259412649	0.283778810232	-0.0563197460509	-0.0540149728956	-0.0501564232699	0.273194201812	-0.426360557862	-0.167289965303	0.364262050673	0.105415692992	0.401363735269	-2.78177167216	87.0789902011	66.7085469961
19	0.385273686237	-0.106093089553	-0.48922195811	0.473197802149	-0.213381670233	0.893233959557	-0.0622736372785	0.317035293611	0.0279646916487	-0.310636413277	-0.106057511063	0.0589305792717	-0.0877172183652	-0.0638772556137	0.108774285833	1.0198670418	-0.312177034162	-0.110361703607	0.811257919239	0.00251983509221	0.331765916918	-5.87166467784	67.2824269629	6.51679826705
20	0.757993843285	0.071776979951	0.018781121058	0.842738808461	0.513936591964	0.67030865176	-0.0218726824647	0.271484411301	-0.390131271764	-0.105766071118	0.0317429229879	-0.165955276457	0.694992922096	0.183600248041	-0.0111105475845	1.14460304561	-0.176019310377	-0.083529210059	0.691254779353	0.0842789323366	0.411231821572	2.67552819475	56.3375178489	25.6537191585
21	1.27442203333	-0.139274481672	0.321289876176	0.623306041239	0.28828768401	0.68168959034	-0.0110470667645	0.416082986277	-0.097340364299	-0.290742336789	-0.0660396400025	0.24194824752	0.305233946225	-0.30027909884	-0.0636555742012	0.679149505261	-0.469791447527	-0.240320941271	0.726102082077	0.145981711159	0.275339525703	-12.4713067318	67.3656712617	25.1467671881
22	0.688246911975	0.373016982429	-0.40763804372	0.560881736068	-0.23397252878	0.243056503288	-0.0107101977836	-0.10586025877	-0.0631401312169	0.0227957636796	-0.0201067438044	0.36386254029	0.114578247407	-0.204763699986	-0.00403564701871	0.53537829354	-0.55786337804	-0.0728666137988	0.652102718407	0.0796746843203	0.477086300438	-23.7861913621	68.0001824028	54.8232730525
23	0.380886142426	0.234468909066	-0.131141225385	0.326783073489	-0.108812290452	0.365565232538	-0.0132265108087	-0.0235107934303	0.194381259697	0.0214288939845	-0.0441560519456	0.201186398999	0.00811211125281	-0.0577979690996	-0.0407013333085	0.365126955849	-0.494517701762	-0.169673537848	0.447530045386	0.0787210283351	0.342033885746	-15.1476103221	76.7183767573	57.7733265355

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 2 through 76 )	A	A	2 - 76	1 - 67
2	2	chain 'A' and (resid 77 through 265 )	A	A	77 - 265	68 - 226
3	3	chain 'A' and (resid 266 through 338 )	A	A	266 - 338	227 - 299
4	4	chain 'A' and (resid 339 through 429 )	A	A	339 - 429	300 - 390
5	5	chain 'A' and (resid 430 through 478 )	A	A	430 - 478	391 - 439
6	6	chain 'A' and (resid 479 through 577 )	A	A	479 - 577	440 - 538
7	7	chain 'B' and (resid 2 through 106 )	B	D	2 - 106	1 - 87
8	8	chain 'B' and (resid 107 through 189 )	B	D	107 - 189	88 - 157
9	9	chain 'B' and (resid 190 through 391 )	B	D	190 - 391	158 - 338
10	10	chain 'B' and (resid 392 through 478 )	B	D	392 - 478	339 - 422
11	11	chain 'B' and (resid 479 through 534 )	B	D	479 - 534	423 - 478
12	12	chain 'B' and (resid 535 through 578 )	B	D	535 - 578	479 - 522
13	13	chain 'C' and (resid 2 through 116 )	C	G	2 - 116	1 - 104
14	14	chain 'C' and (resid 117 through 152 )	C	G	117 - 152	105 - 140
15	15	chain 'C' and (resid 153 through 209 )	C	G	153 - 209	141 - 187
16	16	chain 'C' and (resid 210 through 427 )	C	G	210 - 427	188 - 385
17	17	chain 'C' and (resid 428 through 478 )	C	G	428 - 478	386 - 436
18	18	chain 'C' and (resid 479 through 578 )	C	G	479 - 578	437 - 536
19	19	chain 'D' and (resid 2 through 96 )	D	J	2 - 96	1 - 79
20	20	chain 'D' and (resid 97 through 265 )	D	J	97 - 265	80 - 218
21	21	chain 'D' and (resid 266 through 391 )	D	J	266 - 391	219 - 344
22	22	chain 'D' and (resid 392 through 478 )	D	J	392 - 478	345 - 431
23	23	chain 'D' and (resid 479 through 576 )	D	J	479 - 576	432 - 529

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-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

-
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