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- PDB-7ae5: Structure of Sedimentibacter hydroxybenzoicus vanillic acid decar... -

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Open data

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Basic information

Entry

Database: PDB / ID: 7ae5

Title

Structure of Sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (ShVdcCD) in open form

Components

Phenolic acid decarboxylase
Protein ShdD

Keywords

LYASE / Decarboxylase / Hetero-complex / UbiD

Function / homology

Function and homology information

4-hydroxybenzoate decarboxylase / protocatechuate decarboxylase / 4-hydroxybenzoate decarboxylase activity / protocatechuate decarboxylase activity / 4-hydroxy-3-polyprenylbenzoate decarboxylase activity / ubiquinone biosynthetic process / catabolic process / response to toxic substance / metal ion binding / cytosol
Similarity search - Function

Biological species

Sedimentibacter hydroxybenzoicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.19 Å

Authors

Marshall, S.A. / Leys, D.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Domain mobility and allosteric activation of UbiD decarboxylases
Authors: Marshall, S.A. / Payne, K.A.P. / Leys, D.

History

Deposition	Sep 17, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 25, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	7ae5.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb7ae5.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	7ae5.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/ae/7ae5 ftp://data.pdbj.org/pub/pdb/validation_reports/ae/7ae5	HTTPS FTP

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Related structure data

Related structure data	7ae4C 7ae7C 5m1cS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	7ae7-d 2idb-1 5m1c-1 5m1d-1 5m1b-1 5m1e-1 4b3k-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#118 - Oct 2009 Sodium-Potassium Pump similarity (1)

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Assembly

Deposited unit

B: Phenolic acid decarboxylase

C: Phenolic acid decarboxylase

D: Phenolic acid decarboxylase

E: Phenolic acid decarboxylase

F: Phenolic acid decarboxylase

A: Phenolic acid decarboxylase

b: Protein ShdD

c: Protein ShdD

d: Protein ShdD

e: Protein ShdD

f: Protein ShdD

a: Protein ShdD

hetero molecules

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

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	98.230, 108.300, 111.420
Angle α, β, γ (deg.)	117.720, 101.320, 91.800
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

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Components

#1: Protein	Phenolic acid decarboxylase / PAD / 3 / 4-dihydroxybenzoate decarboxylase / 4-dihydroxybenzoate DC / 4-hydroxybenzoate ...PAD / 3 / 4-dihydroxybenzoate decarboxylase / 4-dihydroxybenzoate DC / 4-hydroxybenzoate decarboxylase / 4-hydroxybenzoate DC / Phenolic acid decarboxylase subunit C Mass: 54020.457 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sedimentibacter hydroxybenzoicus (bacteria) Gene: shdC, ohb1 / Production host: Escherichia coli (E. coli) References: UniProt: Q9S4M7, protocatechuate decarboxylase, 4-hydroxybenzoate decarboxylase
#2: Protein	Protein ShdD / Phenolic acid decarboxylase subunit D / PAD Mass: 7800.174 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sedimentibacter hydroxybenzoicus (bacteria) Gene: shdD / Production host: Escherichia coli (E. coli) / References: UniProt: Q4R102
#3: Chemical	ChemComp-RB / RUBIDIUM ION Mass: 85.468 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Rb
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 804 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56.12 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Molecular Dimensions BCS H2: 0.1 M Hepes, pH 7.5, 30% v/v PEG Smear low

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Data collection

Diffraction	Mean temperature: 77 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9159 Å / Relative weight: 1
Reflection	Resolution: 2.19→70.15 Å / Num. obs: 197121 / % possible obs: 97.03 % / Redundancy: 1.8 % / B_iso Wilson estimate: 43.17 Å² / CC_1/2: 0.984 / R_merge(I) obs: 0.05937 / R_rim(I) all: 0.08396 / Net I/σ(I): 6.59
Reflection shell	Resolution: 2.19→2.268 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.563 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 19440 / CC_1/2: 0.445 / R_rim(I) all: 0.7962 / % possible all: 95.74

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
xia2		data scaling
xia2		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5M1C

5m1c

Resolution: 2.19→70.14 Å / SU ML: 0.3453 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.607
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2625	9805	4.98 %
R_work	0.2233	187239	-
obs	0.2253	197044	97.03 %

Solvent computation

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

Displacement parameters

B_iso mean: 56.9 Å²

Refinement step

Cycle: LAST / Resolution: 2.19→70.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24495	0	18	804	25317

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	25121
X-RAY DIFFRACTION	f_angle_d	0.6162	34276
X-RAY DIFFRACTION	f_chiral_restr	0.0479	3842
X-RAY DIFFRACTION	f_plane_restr	0.0054	4498
X-RAY DIFFRACTION	f_dihedral_angle_d	6.7921	3426

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 (%)
2.19-2.21	0.3579	339	0.3314	6190	X-RAY DIFFRACTION	96.87
2.21-2.24	0.3625	328	0.3411	6149	X-RAY DIFFRACTION	95.67
2.24-2.27	0.3749	340	0.3466	6066	X-RAY DIFFRACTION	94.76
2.27-2.3	0.3632	323	0.3221	6165	X-RAY DIFFRACTION	96.29
2.3-2.33	0.3497	315	0.3072	6188	X-RAY DIFFRACTION	95.42
2.33-2.36	0.3233	319	0.3023	6201	X-RAY DIFFRACTION	96.22
2.36-2.39	0.3238	320	0.3006	6176	X-RAY DIFFRACTION	96.18
2.39-2.43	0.335	285	0.2933	6196	X-RAY DIFFRACTION	95.92
2.43-2.47	0.3205	318	0.2917	6264	X-RAY DIFFRACTION	96.77
2.47-2.51	0.3219	331	0.2821	6227	X-RAY DIFFRACTION	97.05
2.51-2.55	0.3238	293	0.283	6241	X-RAY DIFFRACTION	97.2
2.55-2.6	0.3151	344	0.2793	6297	X-RAY DIFFRACTION	97.39
2.6-2.65	0.3296	341	0.2766	6270	X-RAY DIFFRACTION	97.13
2.65-2.7	0.3318	352	0.285	6152	X-RAY DIFFRACTION	95.96
2.7-2.76	0.2945	333	0.2698	6187	X-RAY DIFFRACTION	97.23
2.76-2.82	0.3188	340	0.2782	6289	X-RAY DIFFRACTION	97.63
2.82-2.89	0.2936	340	0.2721	6278	X-RAY DIFFRACTION	97.74
2.89-2.97	0.3026	326	0.254	6190	X-RAY DIFFRACTION	96.62
2.97-3.06	0.2905	338	0.2469	6231	X-RAY DIFFRACTION	97.05
3.06-3.16	0.2898	334	0.236	6302	X-RAY DIFFRACTION	97.39
3.16-3.27	0.2841	301	0.2426	6298	X-RAY DIFFRACTION	97.86
3.27-3.4	0.2863	311	0.2436	6301	X-RAY DIFFRACTION	97.54
3.4-3.56	0.2609	327	0.2152	6242	X-RAY DIFFRACTION	97.56
3.56-3.74	0.2469	341	0.2015	6298	X-RAY DIFFRACTION	97.53
3.74-3.98	0.2505	303	0.1911	6277	X-RAY DIFFRACTION	97.27
3.98-4.29	0.2107	359	0.1773	6227	X-RAY DIFFRACTION	97.07
4.29-4.72	0.2001	282	0.1705	6371	X-RAY DIFFRACTION	98.49
4.72-5.4	0.2198	369	0.1844	6307	X-RAY DIFFRACTION	98.61
5.4-6.8	0.2392	335	0.1949	6295	X-RAY DIFFRACTION	98.13
6.8-70.14	0.2071	318	0.1787	6364	X-RAY DIFFRACTION	98.57

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	3.23388637455	0.852523900911	1.62030713638	2.69578247172	0.496833504174	3.00996371672	-0.35349133741	0.971589262276	-0.145902266639	-0.530465625694	0.290982722461	-0.116066696109	0.310396949926	0.466195085757	0.0533119364398	0.681743009921	0.0217994517131	0.174188738347	0.649548338142	0.000579111138246	0.306754630809	51.7577218312	17.5024947883	-1.6848641885
2	3.04422753436	-0.103405536037	0.00391685312282	1.10163054755	0.273832741361	1.15712778969	-0.00030038564756	0.553329597838	-0.222787266201	-0.341266259451	-0.0566560443842	-0.0552533989877	0.387316860323	0.046293656317	0.0691126274846	0.67398236714	0.0460257126738	0.096043797665	0.433749102761	-0.0598326669666	0.252568504257	43.1580054498	7.95887932585	2.90235929265
3	3.78177846577	1.14984605443	-0.182084808959	0.873492926996	0.496602975415	3.11149680604	0.146362846657	0.496683382047	-0.525758743931	-0.473652653737	-0.0107174696155	-0.555796839656	0.250942027927	0.507210278474	-0.176332164266	0.594979611104	0.159391231548	0.129155123139	0.524988224996	-0.0519930002475	0.442339415435	65.3202602373	7.8497189397	5.77465431764
4	2.1811480608	2.10930610005	0.674283406681	3.70393431764	-1.94418061965	4.90078224907	0.23319850802	-0.240566650385	-0.670752276507	0.212138464864	-0.0678467415122	-0.283998502595	0.820294232393	0.252433216213	-0.237420884502	0.681849560698	0.150234535267	0.0560095954773	0.430199420929	-0.06995189183	0.509152180444	59.4145176751	0.133566856744	17.0403632997
5	5.64764414661	0.284270722524	0.122796907252	2.5323998644	0.971103798759	1.92138033942	0.187753816402	0.331811393322	-0.683334632292	-0.0324147003508	0.0300379251698	-0.408153353761	0.942859156834	0.267106343523	-0.200823891088	0.857217811017	0.130535119803	0.0716818842733	0.373156385506	-0.098372531444	0.431420439159	52.4840080045	-3.25530975502	8.79836105052
6	2.32731041189	0.167337992706	0.371412161308	1.12558763031	0.42588307742	0.272375436765	0.150703824733	0.184733979524	-0.298873113698	-0.0459123509959	-0.0296618524407	-0.266277191139	0.368947166295	0.0676603546956	-0.12058698764	0.577481724425	0.0532679406202	0.0631481412067	0.370326070605	0.00403653208137	0.334041807629	53.15087094	9.34680166	15.3164463658
7	2.47489877492	0.0293220994736	-0.074172753113	1.24287824787	-0.670460009931	0.740227070937	-0.0441909319711	0.0834882374452	-0.179769694773	-0.105821983413	0.0294696093402	0.022267336575	0.276447960353	-0.107857994089	0.0181840372023	0.523346010501	-0.0326542187577	0.0470231086624	0.351294291511	-0.0072284925656	0.253138595015	29.6416016809	16.6911805845	24.6348679047
8	-0.0015054963891	0.325704281078	0.0286329673062	0.766236811617	-1.17933229331	7.27723442038	-0.241703198974	0.541748222939	-0.0880082811689	-0.45443607375	0.405078767901	0.18942792422	0.566109384719	-0.865807450784	-0.140355007726	0.679874571444	-0.229593328256	-0.0703829174179	0.596471485426	0.00269566272377	0.353674909624	17.1951290678	21.6274345098	11.7945559451
9	2.430934281	-1.68534255968	1.27456158661	3.92983879535	-0.975702493731	7.56247507348	-0.162738221528	-0.412571559898	0.729767197526	0.278116406476	-0.0294677074452	-0.0510002029764	-0.740746379162	-0.183679892967	0.183173256134	0.347528580535	-0.0176249864032	0.0598094562456	0.301347710226	-0.152542604408	0.621657542099	11.2902359271	67.4041366796	67.9629279029
10	2.00974661622	-1.02256571842	0.425474448692	1.44384020854	0.169034376756	1.99712174377	-0.171729359499	-0.629202537925	0.409070947488	0.222336126616	0.181340313982	0.0543162915359	-0.13657777607	-0.182699373002	-0.0146345331976	0.299631341558	-0.0220178365577	0.0372665599661	0.445738757818	-0.156703788732	0.412502398944	7.40973618834	58.803657742	75.2792875818
11	3.95153997139	1.63105398139	-1.79013468419	2.79502635673	-0.898470271523	4.79912255206	0.128810741317	-0.237966209321	0.16208757183	0.108150035381	-0.165600649061	0.138736863297	0.105271261594	-0.560389634356	0.00338241826869	0.227730107003	0.0137368351521	0.0269871928044	0.37470099625	-0.134362316909	0.405999400092	-4.03382618973	52.5354638604	66.3122831474
12	5.83554533654	5.16620635511	1.62356143678	5.70395164269	1.04029757612	5.98631611667	0.318637109393	-0.987941508345	-0.36518967473	0.311384509847	-0.324405830719	-0.0117834044629	1.07262514941	0.0147846254636	0.0139932111832	0.479022600049	0.0642812240953	0.0326629270974	0.599706431946	0.0537876615635	0.557036019079	-9.71934298781	42.2175105407	70.7756913179
13	2.46537520988	-0.676124825483	0.448956824496	0.739524618845	0.0452672313887	1.16822987825	-0.00603733282846	-0.458849646497	0.0422776381849	0.18827525769	-0.060791357266	0.187693348521	0.0162738817218	-0.367300257618	0.0718407534499	0.28772003189	-0.0180136064704	0.0660077705573	0.417194864954	-0.117103111881	0.396801751445	-0.0399955877138	52.0332393732	72.0521145052
14	3.14547414433	-0.341952964451	0.260074058272	1.65934885087	-0.042739782723	2.20796939208	-0.0118717045685	-0.304436738336	0.0532680937435	0.0421815274754	0.0310330259742	0.0454774354614	0.139726606305	-0.121742018676	-0.0238322070791	0.256844181553	-0.040531498465	0.0163994042925	0.255087291502	-0.0318066662372	0.24946055472	23.9063843322	38.530866634	60.923883471
15	1.67517595955	1.05130328841	0.518167928995	3.19989121188	0.684163135921	1.01802736378	0.21674193463	-0.64816626013	0.457060821262	0.328552550708	-0.117494470331	-0.301318881157	-0.000171759999625	-0.0169969497746	-0.0957507404351	0.311227182291	-0.00666963373878	0.0505637887561	0.49882186095	-0.121053255344	0.433915536866	40.6852369061	46.7242666962	64.8077186768
16	2.44557491854	1.37966354347	-0.149403643218	6.07196149343	-0.423344163974	2.17672034984	-0.295491771475	-0.634897557632	1.30864046914	0.266902484457	0.233116317182	0.0306705130372	-0.283693917437	-0.303033046576	0.0713834046819	0.358756602935	-0.00587137624855	-0.00927022596933	0.535171733295	-0.383357797464	1.01180972036	43.048565074	69.5095835125	64.5592763353
17	2.55945848441	1.03360431493	0.893186664403	1.98995327351	0.884398311946	1.18602204998	-0.244505054229	0.0145708162662	1.4549988078	-0.0533807077606	0.0347505427066	-0.00599605660125	-0.254995577148	-0.0111234577319	0.173871940596	0.327093761303	-0.0148532139511	0.00125343042787	0.280008634747	-0.0757518493918	1.08299380284	43.0552618994	72.0883532541	51.5828785582
18	4.48787624557	1.51065657177	2.09757407817	2.42683751411	0.94145906259	2.83916707715	-0.0375315650349	-0.112264937058	1.06295174477	0.0265933011723	-0.0924625612895	-0.278511097529	-0.457203217058	0.556371377616	0.119413643872	0.286392046867	-0.0411145079837	0.00454891062394	0.449449890508	-0.135868785647	0.998477830006	60.1406685379	63.9534490639	56.3713215059
19	5.41862417301	-0.778974667223	-1.88412703097	4.85521091261	0.523480382334	6.5566276513	-0.0163273650503	0.570112931283	0.708743911397	-0.784606037053	0.0493946071279	-0.0536964957058	0.185351256815	0.114890252995	-0.0258322487276	0.375534231263	-0.0515402641335	0.0394082202969	0.377711455454	0.0806804920937	0.80210917174	62.1462452484	60.7929387262	44.3040617961
20	1.80364574538	-0.052236509027	0.370266817341	0.402415627185	0.0705689196285	-0.0370746845063	-0.0350291909569	0.243853133511	1.0482160256	-0.0910365009585	0.0114663981135	-0.0735738051444	-0.150387448636	0.210503043824	0.0167188820795	0.357669986049	-0.0612098647795	0.0165377373346	0.415674016811	-0.00192413647746	1.00119179525	54.3751751773	65.6089308816	48.966862959
21	3.57262125739	-0.20895270012	0.112660447746	2.30814081208	0.289071988386	1.908183172	0.0608338908109	0.202990075001	0.464480434677	-0.042720732376	-0.0167404074372	-0.108302028573	-0.0630552221329	0.00771715575202	-0.0332514416732	0.231831068192	-0.00559604801908	0.053928953226	0.206286906396	0.0198498527473	0.324052595265	30.3748847893	48.8837829623	42.6303869214
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58	3.41457326312	0.14836186085	1.29904217255	2.0023288988	-3.00990846921	6.41340308341	-0.0504181363584	-0.439354875042	-1.09757165432	0.0145748025778	0.512802671444	0.126389912874	1.04420793313	-0.0653148997685	-0.47240385555	0.551003061284	-0.0123660571115	-0.147430988738	0.599498529561	0.0156760324446	0.641466847081	62.1273154821	40.5865468575	62.822846466
59	2.38080413595	1.73299475024	2.16848752213	2.33185035044	-1.31224457442	9.8493237238	0.517804048091	-1.22785089633	-0.12994032895	-0.000142520694983	-0.232385223011	-2.1773775634	1.22925775397	1.7652562045	-0.310490990133	0.528415853344	0.139334711983	-0.000883096669092	0.745244303247	-0.112938015421	0.731854805571	69.3673647521	39.0882560818	56.3560654242
60	7.29959458816	-4.64002576594	3.31774515172	3.93165752402	0.629493638796	9.0444689558	0.0706721232823	0.14534781196	0.743405434362	-1.16240864719	0.23922214002	-0.6419536477	0.282594270226	-0.229292054351	-0.308158344404	0.533196398511	-0.060677225676	0.0945678657895	0.395880581928	-0.121159605608	0.790734106866	68.2761480657	46.89587437	42.8276966882
61	2.09454001523	-0.325413388338	2.52951749187	6.95743868294	0.244414716977	6.49123362749	0.0306105727772	-0.296375271738	-1.79788895741	0.845644007998	-0.391292892813	-0.209035859866	0.588911945119	0.829140792876	0.316618202135	0.674801073871	0.210493720495	0.143032737858	1.1214392701	0.404735471558	0.949513014777	63.8552742966	-4.0346995583	65.6704049792
62	3.75839060823	-0.791466249652	-4.48033748542	0.204261227847	0.899521293413	5.40184016653	0.59581546479	0.487182644988	-0.25003052947	-0.491919081487	-0.49710560275	-0.984033423139	0.200261532001	1.21758176194	0.0274692768256	0.641946637831	0.490880462952	0.0615962472436	1.14619681309	0.500403055832	1.11206514	60.5840563717	-10.8395465347	77.161098882
63	2.00504334899	0.526873029635	1.43270040633	3.63313235005	-3.26603452195	4.9939117075	0.489929154659	0.151550859906	-0.760592807431	-0.281046418264	-0.175010145993	-0.244584931821	1.0179267905	0.714589163151	-0.123263139653	0.976152163461	0.715643270715	0.0904006590527	1.09608398184	0.658180973429	0.775739635177	53.498240433	-20.6237546154	77.6197500964
64	8.44698530795	-2.39676302605	-4.01307992307	0.932605768438	1.36564884698	2.10730693087	-0.464883363188	0.0617124016175	-0.670051533196	0.216262107391	-0.227172911028	-0.546328920335	1.06738450849	1.37365556151	0.637540363204	0.679515967544	0.430239195587	0.0411816867388	1.11407498387	0.318120872209	0.852182280758	59.7944649551	-10.7542941592	72.8095989368
65	2.29822252605	-0.606371897586	0.717190076514	0.211521145012	0.0835725705925	1.92052407789	-0.0912916740474	-0.557718445112	-0.273733257901	-0.336532733776	-0.277146832761	-0.395985880868	0.362169466693	0.700801145516	0.348347908169	0.61648975372	0.166326369312	0.0575139400564	0.776595183492	0.317330376587	0.664049333018	58.0167384546	-5.41701461711	70.0834771551
66	4.5990877339	-1.41004997705	-0.00110256458211	7.86828029356	-3.22678896316	5.05693157526	0.171661607194	0.822702432552	0.106133189839	-0.811814447053	-0.285400617402	-1.00018773604	0.351431510028	0.678029965062	0.109789959313	0.624297993613	0.151818070858	0.166386887421	0.780810439655	0.141248092548	0.647582390795	56.0874710435	-4.88072741497	60.7357727438
67	2.9533887751	2.1455421505	4.01851335859	1.55790474356	2.91672733028	5.46432375976	-0.0227888775176	0.348481834962	1.17384893288	-0.688896223168	0.200054971551	-1.84710118683	-0.436734812607	2.51078985072	-0.204054076674	0.580082241341	0.110125932713	0.264188783162	0.833421913874	0.297992330536	1.6310199886	63.4983033381	9.23729535138	64.9592186357
68	3.68939243521	1.21472924345	2.07597569786	0.79865387634	0.935958795537	1.31629630402	1.05827002192	-0.812629355409	1.32317283206	1.49808574453	-0.916114206694	0.659984625468	-1.91338159792	0.87740697756	-0.059148607142	1.51805757103	-0.385343268151	0.256043029841	0.755999869175	0.0773802757605	0.948005230929	56.2116273807	15.9213562814	74.2484620511
69	1.97354406536	-1.59009559745	0.127825281004	3.41033276441	1.99933195555	2.07822205944	-0.0060153199141	0.1580892417	-0.0231174185173	-0.397854644598	-0.0426696809529	0.4851600776	-0.434690270905	-0.914264803447	0.0492757509805	0.604195774251	-0.203173541391	-0.14625230792	1.77804293944	0.642164697919	0.942473217595	-9.36846592814	31.8070582253	4.88368773245
70	4.32669887829	4.02549227385	0.147737830464	7.53314273059	-2.69629415627	2.12630431431	-0.70412897065	0.839757608944	0.675492112764	-0.227336517978	1.29359088974	0.658331772415	-0.1104284324	-0.673174324778	-0.492434622137	0.481176965492	-0.173547564906	-0.247101991697	1.60335816151	0.406203383912	0.77623540113	-6.6000003625	36.8816750865	-7.50805692665
71	4.16773775841	-1.52234531937	-0.282296564877	3.28618832197	-2.93188656936	3.39332067817	0.487809793941	0.340057388251	-0.397444832251	-0.697869948057	-0.336976067958	0.48756123969	0.508966912182	-1.18821022485	-0.155669888421	1.13483081555	-0.318112584981	-0.595938148347	1.57372271533	0.31761018392	0.474810571993	0.798102105141	32.3898885452	-15.9656777121
72	1.50264761538	-0.531611162621	0.338008436916	0.968898337757	0.226912714228	3.27642528945	0.0632733663991	-0.123052725935	0.328068697579	-0.228173056534	-0.162698515906	0.186602717571	-0.318335731699	-0.294144467962	0.127104114662	0.409129310954	0.00712673969572	-0.614801410709	2.10400478769	0.765455522886	0.202754287503	-4.1771728708	34.2910129945	-0.780734054027
73	1.87622928077	-2.85590671097	-0.0312787443532	4.41266130851	0.0573646573439	0.00674186533096	0.421188081816	0.280511515609	0.105922653557	-0.302435279404	-0.0597474714498	0.935659999745	0.494500783231	-0.664065222046	-0.383846859747	0.728927539927	-0.30253445451	-0.0663150764221	1.30577224481	0.384146567445	0.638000151424	-0.519107896449	25.5194565819	3.49507172182
74	4.58613707851	-1.87051232399	-2.75402640258	2.77591437687	0.894249356977	3.42534484972	-0.39692210989	-0.99948071182	-0.404344354821	1.26846995951	-0.741840136768	1.16170340688	0.372232087645	-0.62346406414	0.81753782138	0.682285305122	0.236882415353	0.233172132282	1.87959865788	0.275681146544	0.577968302502	-5.58057000851	38.0853281674	15.2081076839
75	4.72833913068	-4.58343521495	4.51890772799	7.9743951694	-0.611851858938	8.34048654769	-0.27417967248	0.113253976244	-0.472840858433	0.178746958446	0.174803493046	1.73893358908	1.2937003158	-1.79023555464	0.0548819307637	0.495631514868	-0.258769859638	0.0163917254603	0.885325996809	-0.109499292285	0.726576814369	-22.9496180331	7.24254985249	47.7607136797
76	8.74404769484	-5.2306052806	1.4792319265	4.24340532927	1.97734057128	7.61361248646	0.248992143599	0.428398410208	-1.28862392499	-0.315196855985	-0.068788330317	2.08135068286	0.751203883058	-1.46355261739	-0.253896573379	0.467983539141	-0.1359541802	-0.0425947041488	0.903896731884	-0.0811807988751	0.942781077987	-24.3823011462	-5.57815934861	47.1516027087
77	4.38446176107	4.97535016726	-1.49867009805	5.97820748335	-2.71477653371	3.64519353583	0.582563996257	-1.48627725188	-0.70850850443	1.95867028226	0.091068687151	2.27386597111	0.955333812408	-1.35421053573	-0.537463313604	0.881388501712	-0.397021198387	0.204056430935	0.940928875501	0.246203574464	0.99299152663	-21.8693059416	-12.823803982	56.5630453354
78	8.20450596143	-2.11690820316	-0.58358338351	6.72085407475	-0.101554300599	3.9346082116	-0.409526946473	0.542175591219	-0.460742110909	-0.483753884588	0.720197966082	1.0767009802	1.0503079645	-2.10659549411	-0.396204755767	0.515706099283	-0.316958582345	0.00100297157018	0.873709308147	-0.033819048919	0.593707928482	-20.3820230531	0.316134481667	47.7493389422
79	6.01042329615	1.64728773925	3.73023110095	3.74709698433	4.69784074769	6.54826465715	-0.891787479998	-0.304261437484	-0.207496272163	0.0632222115563	0.266677576232	-0.0338665374642	0.787156714721	-0.448352751604	0.628494073146	0.516146808545	-0.164560793368	0.0429657469071	0.690573687867	-0.0337107072454	0.505369279748	-15.8789301403	4.23899478669	55.7281977628
80	2.10611564251	1.73323339571	1.5857133891	3.63195617063	4.08651082252	4.72223075875	-1.02352077974	0.394889287569	0.934117580351	0.314332629831	-0.731210983079	0.712667450867	-0.474246855435	0.213665993782	1.75693397287	0.492508369855	0.0269897886985	-0.0231960476698	0.580441551507	-0.00167573932671	0.657168548393	-13.3127439548	13.6887518717	46.7966355594
81	9.23331915869	4.07615804607	6.57539435698	1.95332905497	2.93764579214	4.69070673202	-0.456102282334	0.556405202745	0.879308307772	0.0937907208421	-0.195135290186	1.90588406914	-0.596606825105	-1.39573544456	0.610825432502	0.643770329212	0.0338663755276	0.00967021547858	0.819362249296	-0.0157218390682	1.03259977936	-17.3359059679	13.7019692574	36.5356618922
82	2.91253641809	3.23565992046	2.58710738625	3.65980193908	3.35407428769	6.26121562954	-0.539071493201	1.54762493727	-0.0880432732486	-2.87684663402	-0.672914239984	-0.449795389105	-0.414625127437	0.0776208191864	1.17126950404	1.12108922449	0.0170299731535	0.194747684506	0.642552721793	0.128038240658	0.668434756857	-9.9527203025	7.88307198472	30.232285831

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 'B' and (resid 3 through 53 )	B	A	3 - 53	1 - 51
2	2	chain 'B' and (resid 54 through 108 )	B	A	54 - 108	52 - 106
3	3	chain 'B' and (resid 109 through 142 )	B	A	109 - 142	107 - 140
4	4	chain 'B' and (resid 143 through 196 )	B	A	143 - 196	141 - 185
5	5	chain 'B' and (resid 197 through 265 )	B	A	197 - 265	186 - 254
6	6	chain 'B' and (resid 266 through 336 )	B	A	266 - 336	255 - 325
7	7	chain 'B' and (resid 337 through 436 )	B	A	337 - 436	326 - 425
8	8	chain 'B' and (resid 437 through 476 )	B	A	437 - 476	426 - 465
9	9	chain 'C' and (resid 3 through 53 )	C	B	3 - 53	1 - 51
10	10	chain 'C' and (resid 54 through 132 )	C	B	54 - 132	52 - 130
11	11	chain 'C' and (resid 133 through 179 )	C	B	133 - 179	131 - 171
12	12	chain 'C' and (resid 180 through 207 )	C	B	180 - 207	172 - 199
13	13	chain 'C' and (resid 208 through 315 )	C	B	208 - 315	200 - 307
14	14	chain 'C' and (resid 316 through 436 )	C	B	316 - 436	308 - 428
15	15	chain 'C' and (resid 437 through 477 )	C	B	437 - 477	429 - 469
16	16	chain 'D' and (resid 3 through 53 )	D	C	3 - 53	1 - 51
17	17	chain 'D' and (resid 54 through 119 )	D	C	54 - 119	52 - 117
18	18	chain 'D' and (resid 120 through 156 )	D	C	120 - 156	118 - 154
19	19	chain 'D' and (resid 157 through 207 )	D	C	157 - 207	155 - 205
20	20	chain 'D' and (resid 208 through 315 )	D	C	208 - 315	206 - 313
21	21	chain 'D' and (resid 316 through 436 )	D	C	316 - 436	314 - 434
22	22	chain 'D' and (resid 437 through 478 )	D	C	437 - 478	435 - 476
23	23	chain 'E' and (resid 2 through 53 )	E	D	2 - 53	1 - 52
24	24	chain 'E' and (resid 54 through 142 )	E	D	54 - 142	53 - 141
25	25	chain 'E' and (resid 143 through 196 )	E	D	143 - 196	142 - 188
26	26	chain 'E' and (resid 197 through 336 )	E	D	197 - 336	189 - 328
27	27	chain 'E' and (resid 337 through 478 )	E	D	337 - 478	329 - 470
28	28	chain 'F' and (resid 2 through 53 )	F	E	2 - 53	1 - 52
29	29	chain 'F' and (resid 54 through 142 )	F	E	54 - 142	53 - 141
30	30	chain 'F' and (resid 143 through 175 )	F	E	143 - 175	142 - 167
31	31	chain 'F' and (resid 176 through 217 )	F	E	176 - 217	168 - 201
32	32	chain 'F' and (resid 218 through 307 )	F	E	218 - 307	202 - 291
33	33	chain 'F' and (resid 308 through 336 )	F	E	308 - 336	292 - 320
34	34	chain 'F' and (resid 337 through 436 )	F	E	337 - 436	321 - 420
35	35	chain 'F' and (resid 437 through 478 )	F	E	437 - 478	421 - 462
36	36	chain 'A' and (resid 3 through 53 )	A	F	3 - 53	1 - 51
37	37	chain 'A' and (resid 54 through 127 )	A	F	54 - 127	52 - 125
38	38	chain 'A' and (resid 128 through 162 )	A	F	128 - 162	126 - 153
39	39	chain 'A' and (resid 163 through 207 )	A	F	163 - 207	154 - 195
40	40	chain 'A' and (resid 208 through 336 )	A	F	208 - 336	196 - 324
41	41	chain 'A' and (resid 337 through 407 )	A	F	337 - 407	325 - 395
42	42	chain 'A' and (resid 408 through 478 )	A	F	408 - 478	396 - 466
43	43	chain 'b' and (resid 601 through 610 )	b	Z	601 - 610	1 - 10
44	44	chain 'b' and (resid 611 through 628 )	b	Z	611 - 628	11 - 28
45	45	chain 'b' and (resid 629 through 644 )	b	Z	629 - 644	29 - 44
46	46	chain 'b' and (resid 645 through 655 )	b	Z	645 - 655	45 - 55
47	47	chain 'b' and (resid 656 through 665 )	b	Z	656 - 665	56 - 65
48	48	chain 'c' and (resid 601 through 610 )	c	AA	601 - 610	1 - 10
49	49	chain 'c' and (resid 611 through 636 )	c	AA	611 - 636	11 - 36
50	50	chain 'c' and (resid 637 through 644 )	c	AA	637 - 644	37 - 44
51	51	chain 'c' and (resid 645 through 650 )	c	AA	645 - 650	45 - 50
52	52	chain 'c' and (resid 651 through 655 )	c	AA	651 - 655	51 - 55
53	53	chain 'c' and (resid 656 through 667 )	c	AA	656 - 667	56 - 67
54	54	chain 'd' and (resid 601 through 610 )	d	BA	601 - 610	1 - 10
55	55	chain 'd' and (resid 611 through 623 )	d	BA	611 - 623	11 - 23
56	56	chain 'd' and (resid 624 through 636 )	d	BA	624 - 636	24 - 36
57	57	chain 'd' and (resid 637 through 644 )	d	BA	637 - 644	37 - 44
58	58	chain 'd' and (resid 645 through 650 )	d	BA	645 - 650	45 - 50
59	59	chain 'd' and (resid 651 through 655 )	d	BA	651 - 655	51 - 55
60	60	chain 'd' and (resid 656 through 667 )	d	BA	656 - 667	56 - 67
61	61	chain 'e' and (resid 602 through 610 )	e	CA	602 - 610	1 - 9
62	62	chain 'e' and (resid 611 through 616 )	e	CA	611 - 616	10 - 15
63	63	chain 'e' and (resid 617 through 623 )	e	CA	617 - 623	16 - 22
64	64	chain 'e' and (resid 624 through 628 )	e	CA	624 - 628	23 - 27
65	65	chain 'e' and (resid 629 through 636 )	e	CA	629 - 636	28 - 35
66	66	chain 'e' and (resid 637 through 650 )	e	CA	637 - 650	36 - 49
67	67	chain 'e' and (resid 651 through 655 )	e	CA	651 - 655	50 - 54
68	68	chain 'e' and (resid 656 through 665 )	e	CA	656 - 665	55 - 64
69	69	chain 'f' and (resid 603 through 610 )	f	DA	603 - 610	1 - 8
70	70	chain 'f' and (resid 611 through 616 )	f	DA	611 - 616	9 - 14
71	71	chain 'f' and (resid 617 through 623 )	f	DA	617 - 623	15 - 21
72	72	chain 'f' and (resid 624 through 636 )	f	DA	624 - 636	22 - 34
73	73	chain 'f' and (resid 637 through 647 )	f	DA	637 - 647	35 - 45
74	74	chain 'f' and (resid 648 through 660 )	f	DA	648 - 660	46 - 58
75	75	chain 'a' and (resid 601 through 610 )	a	EA	601 - 610	1 - 10
76	76	chain 'a' and (resid 611 through 616 )	a	EA	611 - 616	11 - 16
77	77	chain 'a' and (resid 617 through 623 )	a	EA	617 - 623	17 - 23
78	78	chain 'a' and (resid 624 through 636 )	a	EA	624 - 636	24 - 36
79	79	chain 'a' and (resid 637 through 644 )	a	EA	637 - 644	37 - 44
80	80	chain 'a' and (resid 645 through 650 )	a	EA	645 - 650	45 - 50
81	81	chain 'a' and (resid 651 through 655 )	a	EA	651 - 655	51 - 55
82	82	chain 'a' and (resid 656 through 663 )	a	EA	656 - 663	56 - 63

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi