[English] 日本語

Yorodumi

- PDB-7y8v: Crystal structure of AlbEF homolog mutant (AlbF-H54A/H58A) from Q... -

+
Open data

-
Basic information

Entry

Database: PDB / ID: 7y8v

Title

Crystal structure of AlbEF homolog mutant (AlbF-H54A/H58A) from Quasibacillus thermotolerans

Components

AlbE homolog
AlbF homolog H54A/H58A mutant

Keywords

HYDROLASE / Subtilosin Biosynthesis / M16B Metalloprotease / Macrocyclase

Function / homology

PHOSPHATE ION / : / :

Function and homology information

Biological species

Quasibacillus thermotolerans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Ishida, K. / Nakamura, A. / Kojima, S.

Funding support

1items

Citation

Journal: Structure / Year: 2022
Title: Crystal structure of the AlbEF complex involved in subtilosin A biosynthesis.
Authors: Ishida, K. / Nakamura, A. / Kojima, S.

History

Deposition	Jun 24, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 12, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 11, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Downloads & links

-
Download

PDBx/mmCIF format	7y8v.cif.gz	385.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7y8v.ent.gz	261.9 KB	Display	PDB format
PDBx/mmJSON format	7y8v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7y8v_validation.pdf.gz	464.8 KB	Display	wwPDB validaton report
Full document	7y8v_full_validation.pdf.gz	475.4 KB	Display
Data in XML	7y8v_validation.xml.gz	26.7 KB	Display
Data in CIF	7y8v_validation.cif.gz	36.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y8/7y8v ftp://data.pdbj.org/pub/pdb/validation_reports/y8/7y8v	HTTPS FTP

-
Related structure data

Related structure data	7y8uSC 7y8xC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

-
Assembly

Deposited unit

E: AlbE homolog

F: AlbF homolog H54A/H58A mutant

hetero molecules

89.3 kDa, 2 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)	136.423, 136.423, 119.001
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21
Space group name Hall	P3₁2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3 #4: x-y,-y,-z+2/3 #5: -x,-x+y,-z+1/3 #6: y,x,-z

-
Components

#1: Protein	AlbE homolog Mass: 45754.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Quasibacillus thermotolerans (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A837GIQ1
#2: Protein	AlbF homolog H54A/H58A mutant Mass: 42495.230 Da / Num. of mol.: 1 / Mutation: H54A,H58A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Quasibacillus thermotolerans (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A837GEN5
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.63 Å³/Da / Density % sol: 66.09 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: sodium/potassium phosphate

-
Data collection

Diffraction	Mean temperature: 95 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→44.84 Å / Num. obs: 57022 / % possible obs: 99.8 % / Redundancy: 10.2 % / B_iso Wilson estimate: 50.47 Å² / CC_1/2: 1 / R_merge(I) obs: 0.048 / R_pim(I) all: 0.016 / R_rim(I) all: 0.05 / Net I/σ(I): 25.3
Reflection shell	Resolution: 2.3→2.36 Å / Redundancy: 9.9 % / R_merge(I) obs: 0.458 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 4391 / CC_1/2: 0.971 / R_pim(I) all: 0.153 / R_rim(I) all: 0.483 / % possible all: 99.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS	20190315	data reduction
Aimless	0.7.4	data scaling
MOLREP	11.7.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7Y8U

7y8u

Resolution: 2.3→41.92 Å / SU ML: 0.2933 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 25.3194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2331	2681	4.71 %
R_work	0.1999	54292	-
obs	0.2014	56973	99.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 75.61 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→41.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5863	0	63	58	5984

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0028	6057
X-RAY DIFFRACTION	f_angle_d	0.506	8169
X-RAY DIFFRACTION	f_chiral_restr	0.0414	906
X-RAY DIFFRACTION	f_plane_restr	0.0035	1033
X-RAY DIFFRACTION	f_dihedral_angle_d	12.712	2238

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 (%)
2.3-2.34	0.3462	105	0.2733	2859	X-RAY DIFFRACTION	99.63
2.34-2.39	0.3001	138	0.2549	2820	X-RAY DIFFRACTION	99.63
2.39-2.44	0.2342	139	0.2488	2825	X-RAY DIFFRACTION	99.66
2.44-2.49	0.2742	129	0.2363	2837	X-RAY DIFFRACTION	99.83
2.49-2.55	0.2906	158	0.2335	2798	X-RAY DIFFRACTION	99.73
2.55-2.61	0.2924	169	0.2372	2775	X-RAY DIFFRACTION	99.7
2.61-2.68	0.2599	184	0.2295	2800	X-RAY DIFFRACTION	99.43
2.68-2.76	0.2843	133	0.2384	2833	X-RAY DIFFRACTION	99.76
2.76-2.85	0.2739	111	0.2565	2878	X-RAY DIFFRACTION	99.7
2.85-2.95	0.2925	141	0.2662	2847	X-RAY DIFFRACTION	99.83
2.95-3.07	0.273	123	0.239	2877	X-RAY DIFFRACTION	99.9
3.07-3.21	0.2563	129	0.223	2834	X-RAY DIFFRACTION	99.97
3.21-3.38	0.2523	150	0.2145	2864	X-RAY DIFFRACTION	99.9
3.38-3.59	0.2719	142	0.2071	2866	X-RAY DIFFRACTION	99.97
3.59-3.87	0.2129	127	0.1897	2891	X-RAY DIFFRACTION	99.97
3.87-4.25	0.2101	144	0.1729	2872	X-RAY DIFFRACTION	99.97
4.26-4.87	0.1937	152	0.1503	2884	X-RAY DIFFRACTION	99.93
4.87-6.13	0.2178	150	0.1934	2910	X-RAY DIFFRACTION	99.97
6.13-41.92	0.197	157	0.1789	3022	X-RAY DIFFRACTION	99.72

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	5.02059416236	-3.53246413373	-0.978747921189	8.5775921738	1.99384869451	5.52929839125	0.11046188955	-0.842760932053	0.240550072604	0.896633735578	0.0717943603599	-0.412596194638	-0.43485840811	0.141075437964	-0.220460918773	0.7524566622	0.00867725629783	0.00330565123866	0.66151835373	0.0486771993422	0.386075655597	70.9650922805	1.88139384714	37.1184105384
2	6.36624927694	4.93468303074	-5.68687820414	7.3682119422	-3.084902598	5.57558243169	-1.18483479498	-0.373391866326	-1.03877351948	-0.296754730975	0.293633143914	-0.298579416385	1.31439630572	1.44767683239	0.637507581875	0.561516881805	0.121054214786	0.131177845535	0.442547767167	0.0262692459004	0.597070044212	75.9338204735	-9.11184322938	24.8146725688
3	7.83721414899	-1.2412238288	0.741729622841	7.40388169477	-0.281412737393	7.89248523025	0.705570256783	0.160101136047	1.07731503339	-0.262274486886	-0.588988918574	-0.170398988958	-0.701653318002	0.0637785944012	-0.238892923905	0.51431322138	-0.0182432749893	0.0941262625153	0.205520772426	0.0133453979369	0.368437254428	68.9812657887	5.12331921491	24.6103583501
4	0.584710875503	-0.190512914762	-1.07060324928	0.0524331548842	0.351968742017	2.09673546841	0.327725089378	-1.15583850605	-0.620932713654	1.30134812269	1.98920523049	3.67040474829	-0.0506473531718	-0.654153390969	-2.21072890072	1.0989608762	0.226693151205	0.0779081873909	0.846161775635	0.359327653231	1.83429098307	49.0258775897	12.402610355	18.3717622286
5	2.03735044301	-2.65532054424	1.62544597901	6.45238943178	-1.64125868142	4.93630985244	0.177802321219	0.805397966329	-0.014819633805	-1.30682990987	-0.280693556393	0.0799705426674	0.285015157767	0.0290877178948	0.107110378673	0.844934645309	-0.0577283763389	-0.046460058709	0.433163369806	0.0426862833952	0.405568160199	65.0933666272	11.796376271	9.6348907164
6	3.15423506187	-4.29479139099	-1.1125103797	7.06894822933	-1.13253700526	5.10151346737	-0.342432572764	1.4299935739	0.103347805203	-0.871514463963	-0.0409207733948	-0.26872445001	0.0296428407348	0.159248117392	0.230173502532	0.811635251216	-0.0816190980093	0.0640439877817	0.430131234696	0.0414541116689	0.447982410334	71.9233896863	4.74715325084	14.6279608857
7	7.75982452896	4.54451318968	-2.00257689926	3.8237308792	-3.86987157171	6.73839670641	-0.229033589901	-0.201305336527	1.16780353091	-0.078295845231	0.111438307006	1.69457167747	-1.23553683931	-1.06601762897	-0.0227204212255	0.573163208719	0.0718579425183	-0.136950347145	0.593667161718	0.135295540026	0.982942576132	51.8639238685	4.1317494313	22.0269320111
8	4.07880800024	-5.31333896093	1.10812479393	7.02473308134	-0.954003811908	1.6970286409	-0.0533846771765	-0.331525691065	-0.148565442203	-0.352172378256	0.0406763644095	0.142590436509	-0.0654580793482	-0.165648411873	0.0461023538243	0.686830715206	0.00211046865996	-0.00370532948528	0.342307682738	-0.0189678443188	0.448297350864	68.0742423208	5.39082950749	20.4181220372
9	4.78334289397	-5.03641048503	-2.76225794479	5.57755654026	4.30754998907	7.42101598957	-1.36319609546	-0.31193112859	0.656673105246	1.92220584303	0.72601898155	-1.53519603273	-0.13395258566	1.23597986286	0.408893139305	0.818102456744	0.0522382729919	-0.0590331958535	0.542088072717	0.115968199299	0.780185252775	84.3944152915	3.64901884849	21.8232568453
10	9.58203420604	-5.17600549594	5.0480887612	9.98355864408	-5.2386019308	3.5644991928	-0.225395555295	-0.229547921033	1.12320963117	1.01381553556	-0.443499671913	-1.47430698827	-1.02563189165	0.508573190344	0.717358221959	0.835455392534	-0.124889682623	-0.0153441561067	0.540594553611	-0.0519551569767	0.627338225077	74.5059282868	17.5364221315	17.8161826067
11	3.46524417578	1.34860923935	-2.43384104968	7.21507814851	-0.316887417489	4.55236918207	-0.033196561713	0.200617187624	-0.0151902256497	-2.27984240794	-0.112530699817	-0.301707424904	0.58995921529	0.662900381905	0.31903114811	1.1561405756	0.0552000928526	0.0374387582488	0.503707651097	0.0779598059171	0.467928249001	67.9642925977	17.9681224177	2.81081155841
12	9.21459436678	-0.0537406107779	-4.16997573362	5.75316728303	-5.34916435759	7.41213476842	-0.771583654145	1.41135182562	-1.3594545999	-2.67719063594	0.914197390118	0.925760721203	0.629992227741	-1.18443383815	-0.215337919148	1.52571348334	-0.192821437372	-0.339722021719	0.70625822481	-0.110866788126	0.726710504567	55.4487176676	4.56258894238	1.62318897917
13	9.47929195888	-2.07664686143	-4.95326066956	5.05590718321	1.86270279716	2.79421815558	0.338575798019	0.871151592073	-0.757333910821	-2.51606159572	0.416992660774	1.05404030476	0.465867833209	-1.19139251576	-0.580720804702	1.19824940534	-0.301092393574	-0.587195020331	1.00349181192	0.436083600292	1.57903335411	41.1532338705	-3.67059454501	9.52649236138
14	8.07715644514	3.69963132866	-3.74629333676	4.66876984976	-0.595163987721	3.27266513364	0.0116247984951	0.331331123469	-0.706101446588	-0.75141489019	0.409329502702	1.72496633445	0.205639773264	-1.09056644784	-0.265223317144	1.12034730126	-0.230543332976	-0.443582351209	0.701040130441	0.265170790977	1.19902940193	47.3429636224	8.99296387072	7.29986591923
15	5.74913213151	-1.56336399815	0.764480971788	9.7522141741	-4.88697336051	2.67209204966	0.0267641933374	-0.406297140518	-0.0814618716152	0.00577817661593	0.436299647683	0.361872405682	0.370714061195	-0.767276052823	-0.478418789381	0.579306127158	-0.036679033295	0.0174758522778	0.370123553919	-0.00720044531396	0.303064805282	62.5205010712	20.1275423001	15.2236547787
16	5.96115662512	-2.45953666913	0.71299555563	4.86898687991	0.789745025876	4.57789086989	0.388368463028	-0.112235341115	0.608490898874	0.474244120522	-0.307448767885	-0.53589273154	-0.0317562755524	0.170052968681	-0.0759808196964	0.687407533329	0.0167187700391	0.0880673853668	0.364369493159	-0.0585816235725	0.525227945289	69.1394003707	3.95532407002	28.7290408474
17	6.39403526951	1.98251031471	5.24443461179	5.72496037426	-1.83103273797	6.63471877895	-0.0373400818837	-0.339159274894	0.119106283015	-0.43366195422	-0.658133284053	-3.27406139863	0.884151762164	2.77145344811	0.967070172205	0.761285451265	0.108387743862	0.147465014304	0.684865490372	0.13231280149	0.623468673742	77.2993683432	-4.99942899215	30.4833270004
18	5.89198470565	-4.64274740993	-4.19013463429	5.12634352241	0.388742934214	8.83076940668	0.301613026042	0.677018957162	-0.0808934208293	0.125371678305	-0.960603840318	0.357765368913	-1.05775759002	0.375157956942	0.626123702704	0.658948675106	0.0765545729342	0.0386150200493	0.561031265613	-0.0338799974466	0.359178569979	69.954970469	0.739240911002	32.9074696719
19	4.51433123631	2.94101861159	3.91803285635	1.92513951978	2.38757916581	3.25046728482	0.0372306266721	0.052926972112	0.691897914369	-0.0359616422575	0.0717869997617	1.63986769539	-0.641625364375	-0.412582878211	0.051110746691	0.791001858972	0.115214444116	-0.0765797773688	0.777961837132	0.182208703762	1.42807566733	48.2222227132	2.83922007743	27.9382799088
20	6.59653294738	-3.38495792539	-4.132811986	3.99045027117	2.8463841161	2.82455114717	-0.368025519005	0.998211246414	-1.13849087282	-0.839316942079	-0.228444832377	1.42514300593	-0.163340904917	0.543038843931	0.386712940028	0.947350464796	-0.0649634531809	-0.455202785821	1.31638013067	-0.14097873053	1.48458164904	33.4373352329	-7.46696479815	3.18516966337
21	5.88428709412	0.375089951507	2.57143238445	4.97539571145	-0.569687230988	7.52638274812	-0.500573304798	-0.180758044752	0.485844646136	-0.587538334342	0.3728980684	1.19409393585	0.00441153612529	-0.662799345138	0.191212391215	0.744793391153	0.103602349767	-0.0303465143022	0.665864064246	0.202085750788	1.24438921355	40.0985805666	-10.1154847483	21.4160942946
22	8.43495082458	4.65025385445	4.79557337258	4.23645678603	4.02653925634	4.0945304317	-0.454107114074	0.420718891352	0.0971553255223	-0.0282987670088	0.371586958033	2.0620285219	0.0122716055607	0.941730540759	0.00689931029218	0.575331506699	0.00836371826337	-0.0183159984087	0.532375427817	0.069988169694	0.640088430146	48.5784723175	-15.726761144	24.5900593622
23	3.23478097412	3.90838788421	3.9892218094	5.0182376397	4.99049340919	4.96734362171	-0.392215800132	-0.00927407941665	-0.869306413057	-0.883943147702	0.285015348983	-2.48506869748	0.0385434007768	-0.0444845007829	0.0971763636134	1.76727995822	-0.0569383119523	-0.225143771138	1.04239295183	0.027546916777	1.38923233236	43.7549950858	-27.686004674	12.3731818042
24	7.39299944843	-0.261687292575	-2.45013945066	0.974034897308	2.55482645963	7.36131525515	0.249247519194	0.993824216635	0.843736920295	-1.68000384161	0.651350137137	0.751640444728	-0.294364305503	0.455838994372	-0.804488191541	1.20442605202	-0.131398836856	-0.375487483559	0.725707385282	0.243757306725	0.958282562909	47.2917274555	-13.1112578401	14.6475528368
25	4.39165475232	0.944847251116	1.22123010131	8.47334020196	2.5873550878	6.83153666768	0.555914490218	0.0378178303005	0.352847389443	-0.934747612016	-0.319992276159	-0.365203362305	-0.853432635419	0.490704973814	-0.271722560267	0.633234584086	-0.063872786868	-0.152458743525	0.700172855816	0.267571527105	1.55185170096	44.7226140914	-4.39157083678	20.6453251709
26	8.95524073482	0.848007126495	-0.754708723062	1.57244793462	2.77050889325	8.01757284907	-0.782863377768	2.54392115251	0.685832297223	-2.65820599849	1.83473948571	0.825717863558	1.05038804196	-1.07537899442	-0.838948645402	1.3954612377	-0.477715043938	-0.506324791854	1.09107620199	0.273710448434	1.1414203763	42.4467314214	-14.4606539107	10.8870226687
27	6.14018622005	-1.63061027886	3.66140304924	2.12612351099	-0.136290033425	2.6644763113	0.14440929258	0.61801904662	0.197032812774	-1.31336024267	0.0157071641498	1.63261544637	1.80140339101	-1.2023521926	-0.0731247516249	1.15866679473	-0.278492825686	-0.465997543219	0.988232092027	0.253129840724	1.33281644222	34.1848044237	-22.1678557765	14.0487772556
28	9.50185491292	7.4580456903	-3.10649084826	7.50635993845	-3.58700881559	3.5672783611	-0.223729812754	0.741189979882	0.0369573425176	-0.528634620151	0.449184956828	-0.123309276608	-0.289744061278	-0.461764237471	-0.212287672093	0.655586281449	-0.0141554049212	0.0694745832613	0.373167141141	-0.0293249944731	0.383582015369	58.1229205123	-20.4081535925	24.953655192
29	8.96527732533	0.969123161672	-4.56790439692	6.52013882793	0.603220714066	2.71056094334	-0.315144715378	0.290797859577	-0.526838141533	-1.01125798562	-0.252484959038	0.725956809173	-0.11542710547	-0.289992501985	0.660463147695	0.580782612369	0.0369707737589	-0.0399419711664	0.31783347433	0.0295307774965	0.505881533037	63.5715705995	-4.31014378856	24.7848530368
30	5.9505195382	5.31998675279	-4.73376411147	5.04674141693	-3.25848250235	6.64753908805	0.769888075153	-0.217662983745	0.675372931931	1.68365411936	-0.218717264681	0.597733599579	-0.992844248113	-0.692562547318	-0.448686072872	1.01761072318	0.152066239658	0.0442601783958	0.573038052424	-0.183483578451	0.770372158703	58.3236102029	-5.45731103183	34.2130509448
31	5.79719432534	5.43281071768	3.79637074304	5.28061340411	2.75779834418	8.82728220428	0.691470125186	-1.32704090933	0.144656901549	1.40210935577	-0.419429398464	0.395287654274	0.720951745174	-0.196963185644	-0.264644039118	0.668755866334	-0.000182527809661	0.0386692251515	0.414412754242	-0.0299204566083	0.416306483051	58.6386350414	-15.7998144591	33.8646812166
32	3.36819509303	-2.77219950244	-1.0068015685	3.49602672249	-2.33587788557	8.48650771272	0.644888563516	0.238099224671	0.869852650683	0.871173570359	-0.55411057148	2.53282060591	-0.704840252683	-0.731198599137	-0.00374377315703	0.612462520494	-0.0880733708119	0.191187329695	0.58036583249	0.00886785119172	1.10695452983	40.9125116762	-18.1624464398	31.1908532369
33	3.20070629871	-0.650513602697	2.19330687442	3.35795264979	-1.92631055509	4.80283886542	0.0400784637221	0.311812056435	1.03529825963	-1.03743669298	0.804998011355	1.80599874686	-0.17629671537	-0.736053077831	-0.717239454182	0.963250931492	-0.203911034585	-0.346459613568	0.753804760744	0.357816284385	1.70934193609	34.567183744	-10.6642741355	14.3167490005
34	2.15042561676	2.17893589173	0.0106925008971	8.74598884689	2.27546218402	8.75837988275	-0.228723574036	0.466467036081	0.605322929498	1.58283878853	0.446018164944	-1.04758813228	-0.149218653067	0.333162828661	-0.171464776529	0.496243880793	-0.107780745345	-0.0332907104507	0.817033966896	-0.0258957540937	0.726306288354	89.4721258546	-11.9916929939	19.6671986235
35	3.51858791483	-0.676163739788	-0.597020096054	6.94713124103	2.35691142186	4.86876710848	0.113750881758	-0.596329329562	0.211501777472	-0.792614743077	-0.0930163366523	-0.209231857329	-0.380069231059	0.846821409851	-0.00984376986383	0.354342560055	-0.0865717804302	-0.00701845533296	0.596414858474	-0.0105787564699	0.323818136421	83.5185645074	-28.8465304796	17.992966713
36	2.90058750556	3.52735479361	3.34196589425	4.49807682006	3.99124879389	3.95707359582	-1.08963264024	-0.705812872391	0.314605763697	1.50216440058	-0.0385966639631	-0.479806859576	0.213735879424	1.00985760859	0.862289854276	0.740106492089	-0.0139166704864	-0.00481345823516	0.579568039929	-0.0852076674477	0.578454786447	72.662788708	-16.9133231172	27.1038057086
37	6.16165786718	0.547458924114	-2.17740739439	2.33286461792	-2.87624193559	3.93731426562	0.11406924176	0.344233278001	0.122947371315	-0.457189148373	0.371578612443	-0.144308328336	-0.149942457497	0.191225519457	-0.350855561055	0.473259877856	0.0146351824644	-0.00679652420541	0.288704234256	0.00770837525598	0.319955096122	74.447449645	-30.6984568003	7.21041448409
38	9.79331964101	5.18049805274	-3.26085612783	4.56418301725	0.505430298241	3.79741184403	-0.880370229713	1.40843173971	-0.181666916051	-1.18209715665	0.261264790191	-1.09432348647	-0.0371500173435	1.21713483353	0.469477416038	1.10512126205	-0.148352489487	-0.0510397545623	1.13972105829	0.0637316013708	0.791265931943	72.0000974628	-36.2335480169	-9.03145648722
39	1.63202597524	0.762331824391	-0.185589066879	3.81552587931	1.73763794141	5.41146461444	-0.0103228092186	-0.00574772703798	-0.0811957487016	-0.0865571257949	-0.125470042827	0.306055097712	0.299318319735	-0.375858689974	0.145695125289	0.278886204289	-0.0199282350403	-0.0259351837903	0.312191374648	-0.00475212048943	0.261692314856	65.9868077785	-35.2512564941	12.3931258509
40	6.51477720623	-2.12612300394	0.856884768596	4.3891649457	-4.10314327363	4.2251690905	-0.417246603115	0.130198879334	0.221455917893	-1.22844824415	0.679800723048	0.969757442996	0.301183406213	-1.63271087444	-0.393107590285	0.758767459016	-0.0849739110081	-0.203722420675	0.84243880264	-0.11876668096	0.546873304347	55.9855286034	-37.746273002	-2.57491285989
41	3.79640275129	2.08571226041	-3.44600839014	7.06349921532	3.93252464376	8.84774223244	0.505223362006	0.405659558611	0.276151722408	-0.67345273104	0.27940316709	0.960336292867	-2.71005587449	0.679045725921	-0.598085152694	1.11960066526	-0.1114349268	0.0640237299493	0.588416420157	-0.0913975789452	0.490937664752	63.6058015887	-41.3631012755	-8.85763753826
42	3.92979554623	0.578608157643	0.0566162270238	5.3692002606	2.92580911092	3.47926274064	-0.0263014052119	0.301355349698	-0.508778351886	-0.354199729765	0.119062971642	-0.170891214588	0.0164776978902	0.243676629521	-0.123376318379	0.3734025801	0.0113455785795	0.00679517053976	0.354040961336	0.0223230551214	0.26172945403	75.1546960031	-39.2683958431	5.82679596782
43	6.42641778366	-2.98419103492	-1.19283517581	7.60379961652	-1.80621590282	2.95661425666	-0.106764305678	-0.914985426679	-0.132757165164	1.5093037184	0.412962064839	-0.0772409922178	0.124411712693	0.723684828344	-0.294817568613	0.429778318351	0.000267319209885	-0.00169518898603	0.524488347096	0.0578312570639	0.34061752184	78.9632409585	-35.1531404949	23.96698221
44	3.77499432335	0.0642318492066	1.82680933857	3.177650928	-1.53431510698	5.81321728924	-0.100310086399	1.06151457223	0.22521994851	-1.16539734009	0.109430966317	0.169553816586	0.164639032368	1.33730103017	0.0713046555673	1.10344157606	-0.121115547754	0.000379729772726	1.00178326233	0.02670576709	0.586004630277	78.3842246571	-35.9187193813	-4.01275953017
45	9.33995897206	-3.72381256991	-0.806982717852	8.63058055189	-0.846704012626	8.51964725922	0.0053921626194	0.722588330219	-0.275781290123	-0.188132260143	0.446104824444	2.20356376941	0.160858625675	-1.50990032229	-0.607742373082	0.918280276501	-0.0385573865441	-0.0510844700542	0.79887545368	0.19613418823	0.802836305093	76.9102844862	-19.5781364089	-16.8988532
46	7.561243535	4.67341651237	-6.46238858777	2.95987063695	-4.06148886966	5.62503864779	-0.208124329468	-1.70831603662	0.422181144044	0.420976401846	-1.06748672498	-0.964942699612	-0.518295850188	1.71488273482	1.4134899948	0.502819718841	0.0115058989414	0.0313261663018	0.715473752901	0.0472502854124	0.709903973631	91.9463567518	-18.0964357423	-5.62782907347
47	3.93567036697	-1.46693068512	-0.405817503966	8.29755438811	-3.09485307872	4.87499341468	0.391992739369	-0.116749052166	0.127082424865	-0.0789233534415	-0.116321659577	0.826323789505	-0.366672140207	0.243139338656	-0.150295192263	0.54355999473	0.00244147062935	0.0624213997293	0.33007490139	0.0137865698451	0.383003910703	86.7124530627	-14.4078165145	-1.66830530903
48	2.18733190391	-3.50985678372	4.5665108762	5.80745078986	-7.53223533957	9.75105126167	0.83826261948	0.254265114964	1.51083708689	1.27232757828	0.826975580595	0.88694074018	-2.00883686625	-0.973771170499	-1.36379589836	1.06367641078	0.118338901749	0.280840835826	0.610976941064	0.269819502702	0.760403623195	78.1930452669	-1.46544392585	-9.1919310783
49	0.160923033218	-1.08156073737	0.724468787813	6.66837678682	-4.63931251851	3.22697534497	0.180022015179	0.0030252566306	-0.216526616134	0.259825127462	1.35714904496	2.52179063519	0.0532447450561	-1.36948709268	-0.998238782885	0.83751681373	0.213893042114	0.0875633289163	0.945392641065	0.543924758577	1.60565181595	72.5428942804	-4.28381291036	-14.2242750364
50	5.99162051603	-0.421585592097	-0.508222030691	7.7771528456	-4.2257095028	2.38365934045	0.257664592542	0.38128189858	-0.43376423515	-0.433510098227	-0.0476201862541	0.573855087957	0.940137736691	-0.0651458731768	-0.20236111599	0.555043627072	0.0504538888024	0.0831826854625	0.362625459838	-0.0130501075011	0.428770738215	81.6277363691	-21.3322418333	-5.16231995918
51	9.86221106275	3.74530162305	-0.182163101867	8.0765718197	-0.684182678847	5.78737439652	0.167590490463	1.26666654363	0.967268204576	0.498940609828	0.280584213377	0.0176963509523	0.0457536725409	0.292999770681	-0.393926213183	1.03549691235	0.166116297584	0.0534340682782	0.623677202971	0.220813842863	0.572995928283	81.415260323	-5.94169910812	-17.4258195747
52	5.0613255494	2.13342455442	-1.21917347827	9.53389975377	-6.65424094969	4.74962503229	-0.135898167137	0.214848549312	0.513946102887	0.213100070993	0.447060565391	-0.521241844215	-2.56698372955	-0.285220849673	-0.201343939097	1.11376391137	-0.202178304576	0.00796733569772	0.534089159083	-0.060819750831	0.636116012625	87.2112083476	-1.57702607345	0.875511961155
53	5.35496848492	2.68204722863	-1.84038048234	4.20187199977	-4.04370068375	4.0211585137	0.0755239789707	0.0422140198943	0.235818026114	-0.206123837293	-0.262432494665	1.10016207319	0.0113251864112	-0.683344824752	0.166454522529	0.522882340815	-0.0464183941275	0.0752831291789	0.358168283627	-0.0666187798969	0.427252095592	77.8353304331	-10.1424314221	14.0390448231
54	4.435278596	2.79557464788	0.735812488838	4.30123515678	-1.44770559583	6.55262553742	0.061822620303	-0.161139994032	0.130617420372	-0.234204655849	-0.238533929138	0.0493770624141	0.1766343279	0.0923311674661	0.198702680811	0.456184840567	-0.014934418983	0.0138405416351	0.367898355425	0.0142058046565	0.381461825479	80.7929862789	-19.9756398274	9.25249461466
55	3.36006077981	1.32360081918	-0.508685336677	6.68144814095	-4.43140521486	8.40428314111	0.0864293224316	0.186772840185	-0.104807177501	-0.231001661479	-0.370440056776	-0.26384119534	-0.553292321933	0.576514670635	0.316199033401	0.501444322749	-0.105733878117	0.035571899706	0.605694175957	-0.0238491074156	0.501728780991	92.3429985564	-11.8281724143	6.82585789841
56	5.37319759993	2.57079872697	5.45373958169	6.9321837147	2.66537837195	5.5381368604	0.291944561381	1.01340969201	-0.386768532584	-0.235270327106	0.284426359295	-0.132264468605	0.735524774207	1.9288834857	-0.372340465732	0.75298191989	-0.0040562173053	0.0798675237272	0.696260739513	0.0570293964941	0.568973820494	90.5107870872	-11.4765256496	-14.8577867114

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 'E' and (resid -2 through 7 )	E	A	-2 - 7	1 - 10
2	2	chain 'E' and (resid 8 through 13 )	E	A	8 - 13	11 - 16
3	3	chain 'E' and (resid 14 through 21 )	E	A	14 - 21	17 - 24
4	4	chain 'E' and (resid 22 through 32 )	E	A	22 - 32	25 - 35
5	5	chain 'E' and (resid 33 through 50 )	E	A	33 - 50	36 - 53
6	6	chain 'E' and (resid 51 through 63 )	E	A	51 - 63	54 - 66
7	7	chain 'E' and (resid 64 through 69 )	E	A	64 - 69	67 - 72
8	8	chain 'E' and (resid 70 through 77 )	E	A	70 - 77	73 - 80
9	9	chain 'E' and (resid 78 through 90 )	E	A	78 - 90	81 - 93
10	10	chain 'E' and (resid 91 through 101 )	E	A	91 - 101	94 - 104
11	11	chain 'E' and (resid 102 through 109 )	E	A	102 - 109	105 - 112
12	12	chain 'E' and (resid 110 through 125 )	E	A	110 - 125	113 - 128
13	13	chain 'E' and (resid 126 through 140 )	E	A	126 - 140	129 - 143
14	14	chain 'E' and (resid 141 through 160 )	E	A	141 - 160	144 - 163
15	15	chain 'E' and (resid 161 through 178 )	E	A	161 - 178	164 - 181
16	16	chain 'E' and (resid 179 through 184 )	E	A	179 - 184	182 - 187
17	17	chain 'E' and (resid 185 through 188 )	E	A	185 - 188	188 - 191
18	18	chain 'E' and (resid 189 through 192 )	E	A	189 - 192	192 - 195
19	19	chain 'E' and (resid 193 through 206 )	E	A	193 - 206	196 - 209
20	20	chain 'E' and (resid 207 through 217 )	E	A	207 - 217	210 - 220
21	21	chain 'E' and (resid 222 through 234 )	E	A	222 - 234	222 - 234
22	22	chain 'E' and (resid 235 through 250 )	E	A	235 - 250	235 - 250
23	23	chain 'E' and (resid 251 through 264 )	E	A	251 - 264	251 - 264
24	24	chain 'E' and (resid 269 through 276 )	E	A	269 - 276	265 - 272
25	25	chain 'E' and (resid 277 through 280 )	E	A	277 - 280	273 - 276
26	26	chain 'E' and (resid 281 through 286 )	E	A	281 - 286	277 - 282
27	27	chain 'E' and (resid 290 through 308 )	E	A	290 - 308	286 - 304
28	28	chain 'E' and (resid 309 through 330 )	E	A	309 - 330	305 - 326
29	29	chain 'E' and (resid 331 through 341 )	E	A	331 - 341	327 - 337
30	30	chain 'E' and (resid 342 through 346 )	E	A	342 - 346	338 - 342
31	31	chain 'E' and (resid 347 through 359 )	E	A	347 - 359	343 - 355
32	32	chain 'E' and (resid 360 through 369 )	E	A	360 - 369	356 - 365
33	33	chain 'E' and (resid 370 through 378 )	E	A	370 - 378	366 - 374
34	34	chain 'F' and (resid 2 through 14 )	F	B	2 - 14	1 - 13
35	35	chain 'F' and (resid 15 through 29 )	F	B	15 - 29	14 - 28
36	36	chain 'F' and (resid 30 through 34 )	F	B	30 - 34	29 - 33
37	37	chain 'F' and (resid 35 through 46 )	F	B	35 - 46	34 - 45
38	38	chain 'F' and (resid 47 through 51 )	F	B	47 - 51	46 - 50
39	39	chain 'F' and (resid 52 through 117 )	F	B	52 - 117	51 - 116
40	40	chain 'F' and (resid 118 through 133 )	F	B	118 - 133	117 - 132
41	41	chain 'F' and (resid 154 through 164 )	F	B	154 - 164	133 - 143
42	42	chain 'F' and (resid 165 through 186 )	F	B	165 - 186	144 - 165
43	43	chain 'F' and (resid 187 through 200 )	F	B	187 - 200	166 - 179
44	44	chain 'F' and (resid 201 through 220 )	F	B	201 - 220	180 - 199
45	45	chain 'F' and (resid 221 through 227 )	F	B	221 - 227	200 - 206
46	46	chain 'F' and (resid 228 through 232 )	F	B	228 - 232	207 - 211
47	47	chain 'F' and (resid 233 through 243 )	F	B	233 - 243	212 - 222
48	48	chain 'F' and (resid 244 through 254 )	F	B	244 - 254	223 - 233
49	49	chain 'F' and (resid 255 through 260 )	F	B	255 - 260	234 - 239
50	50	chain 'F' and (resid 261 through 274 )	F	B	261 - 274	240 - 253
51	51	chain 'F' and (resid 275 through 294 )	F	B	275 - 294	254 - 273
52	52	chain 'F' and (resid 295 through 309 )	F	B	295 - 309	274 - 288
53	53	chain 'F' and (resid 310 through 319 )	F	B	310 - 319	289 - 298
54	54	chain 'F' and (resid 320 through 334 )	F	B	320 - 334	299 - 313
55	55	chain 'F' and (resid 335 through 347 )	F	B	335 - 347	314 - 326
56	56	chain 'F' and (resid 348 through 364 )	F	B	348 - 364	327 - 343

+
About Yorodumi

-
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