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- PDB-8e1u: Propionibacterium freudenreichii PPi-dependent PEPCK in complex w... -

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Open data

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Basic information

Entry

Database: PDB / ID: 8e1u

Title

Propionibacterium freudenreichii PPi-dependent PEPCK in complex with malate

Components

PPi-dependent PEPCK

Keywords

LYASE / Allosteric inhibitor

Function / homology

D-MALATE / Hypothetical secreted protein

Function and homology information

Biological species

Propionibacterium freudenreichii subsp. shermanii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

McLeod, M.J. / Holyoak, T.

Funding support

Canada, 1items

Citation

Journal: Proteins / Year: 2023
Title: Biochemical, structural, and kinetic characterization of PP i -dependent phosphoenolpyruvate carboxykinase from Propionibacterium freudenreichii.
Authors: McLeod, M.J. / Holyoak, T.

History

Deposition	Aug 11, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 7, 2023	Provider: repository / Type: Initial release
Revision 1.1	Aug 23, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Oct 25, 2023	Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.details

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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	8e1u.cif.gz	4.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8e1u.ent.gz	2.9 MB	Display	PDB format
PDBx/mmJSON format	8e1u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8e1u_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	8e1u_full_validation.pdf.gz	2.1 MB	Display
Data in XML	8e1u_validation.xml.gz	291.4 KB	Display
Data in CIF	8e1u_validation.cif.gz	404.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e1/8e1u ftp://data.pdbj.org/pub/pdb/validation_reports/e1/8e1u	HTTPS FTP

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Related structure data

Related structure data	6k31S S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (1) #21 - Sep 2001 Antibodies similarity (1)

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Assembly

Deposited unit

A: PPi-dependent PEPCK

B: PPi-dependent PEPCK

C: PPi-dependent PEPCK

D: PPi-dependent PEPCK

E: PPi-dependent PEPCK

F: PPi-dependent PEPCK

G: PPi-dependent PEPCK

H: PPi-dependent PEPCK

hetero molecules

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

A: PPi-dependent PEPCK

hetero molecules

F: PPi-dependent PEPCK

hetero molecules

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

B: PPi-dependent PEPCK

H: PPi-dependent PEPCK

hetero molecules

defined by author&software
255 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

C: PPi-dependent PEPCK

hetero molecules

D: PPi-dependent PEPCK

hetero molecules

defined by author&software
255 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

G: PPi-dependent PEPCK

hetero molecules

E: PPi-dependent PEPCK

hetero molecules

defined by author&software
255 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	134.131, 146.952, 151.094
Angle α, β, γ (deg.)	82.700, 84.000, 70.800
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	PPi-dependent PEPCK Mass: 127271.562 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria) Gene: PFREUDJS001_000139 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A160VN62
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID Mass: 134.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₆O₅ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1220 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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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: 2.75 Å³/Da / Density % sol: 55.34 % / Description: Plates
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES, pH 7.5, 200 mM magnesium chloride, 10% ethylene glycol, 7.5% isopropanol, 10-20% PEG2000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 5, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.65→74.8 Å / Num. obs: 304269 / % possible obs: 97.1 % / Redundancy: 3.8 % / B_iso Wilson estimate: 45.18 Å² / CC_1/2: 0.93 / R_merge(I) obs: 0.118 / R_pim(I) all: 0.07 / R_rim(I) all: 0.137 / Net I/σ(I): 10.4
Reflection shell	Resolution: 2.65→2.75 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.757 / Mean I/σ(I) obs: 2 / Num. unique obs: 29413 / CC_1/2: 0.72 / R_pim(I) all: 0.453 / R_rim(I) all: 0.884 / % possible all: 93.8

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
DIALS		data reduction
DIALS		data scaling
MOLREP		phasing
REFMAC	8.0.006	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 6K31

6k31

Resolution: 2.65→74.77 Å / SU ML: 0.3372 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.6035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.223	2000	0.66 %
R_work	0.1806	301887	-
obs	0.1809	303887	96.95 %

Solvent computation

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

Displacement parameters

B_iso mean: 55.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→74.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	71188	0	62	1220	72470

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0024	72999
X-RAY DIFFRACTION	f_angle_d	0.4909	99209
X-RAY DIFFRACTION	f_chiral_restr	0.04	10717
X-RAY DIFFRACTION	f_plane_restr	0.0043	13178
X-RAY DIFFRACTION	f_dihedral_angle_d	11.4277	27179

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 (%)
2.65-2.72	0.3339	136	0.274	20453	X-RAY DIFFRACTION	91.94
2.72-2.79	0.2979	140	0.2532	21269	X-RAY DIFFRACTION	95.68
2.79-2.87	0.2976	142	0.2399	21349	X-RAY DIFFRACTION	95.91
2.87-2.96	0.3067	141	0.2389	21390	X-RAY DIFFRACTION	96.15
2.96-3.07	0.3204	143	0.2367	21426	X-RAY DIFFRACTION	96.4
3.07-3.19	0.2759	143	0.224	21564	X-RAY DIFFRACTION	96.75
3.19-3.34	0.2665	142	0.2106	21574	X-RAY DIFFRACTION	96.97
3.34-3.51	0.237	143	0.1968	21596	X-RAY DIFFRACTION	97.27
3.51-3.73	0.2429	144	0.1871	21710	X-RAY DIFFRACTION	97.58
3.73-4.02	0.2116	144	0.1616	21724	X-RAY DIFFRACTION	97.91
4.02-4.43	0.208	145	0.1499	21869	X-RAY DIFFRACTION	98.16
4.43-5.07	0.1786	145	0.138	21908	X-RAY DIFFRACTION	98.51
5.07-6.38	0.1707	146	0.1681	22036	X-RAY DIFFRACTION	98.96
6.38-74.77	0.1572	146	0.1404	22019	X-RAY DIFFRACTION	99.12

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	1.84753279029	0.0131939252625	-0.0490669253798	1.58378422711	0.809204487952	0.847394489171	-0.0509692602472	-0.163302473564	0.207869145502	0.184558902106	-0.0803381741908	0.407911439843	-0.0538979003879	-0.0895923009834	0.127745240177	0.429019375123	0.0588570800111	0.0507656064336	0.325824291499	-0.0767497177038	0.426683413128	-2.10557637796	19.9408852903	23.3194009152
2	1.02277919113	-0.29236806731	0.137953296563	1.32943524694	0.59476279683	1.12969488466	-0.182257405637	-0.227580547502	0.0448772027111	0.223764985453	-0.0208921015133	0.565442257351	-0.0202236357999	-0.203358076235	0.169771188023	0.350744918518	0.0289113217761	0.0666155626859	0.296512734921	-0.0170452595898	0.515847902038	-11.1066462423	8.61277223427	13.7292069732
3	3.53789650683	-1.76769829869	0.433350538554	4.42704893674	-1.74388271823	2.02781680794	0.00798393033085	0.545842843925	0.36888255379	-0.158498834493	0.0903649469307	0.00454084560449	-0.164556144295	-0.00313030549489	-0.090005042252	0.462827074769	-0.132243495615	-0.0851728958646	0.507919637968	0.0991246844297	0.295867491809	25.5032578718	10.8399159727	-19.7396907741
4	3.54178767416	-1.34870083331	-2.51566993238	1.19054381396	1.01338399168	2.95032276288	-0.152197231663	0.218037302728	-0.219256339431	-0.0440373217816	-0.00862260075034	0.0475200550714	0.354340110429	0.188136313577	0.160711920348	0.405554386458	-0.0275064260468	-0.0400132077368	0.412738864932	0.00543646734326	0.299707273654	20.5457623385	-15.0281225921	-23.17985808
5	0.740218234633	-0.138543925472	0.291902238591	0.633958238315	0.219037391936	0.967177523461	-0.12642385869	0.0550872694251	0.0208345580259	0.0352986669375	-0.00171739650143	0.0426593603913	0.0797627826622	0.119646797191	0.131094747826	0.385434434966	-0.00357086614606	0.0340257987243	0.29801955255	0.0408804168416	0.344772467679	15.2089016363	-4.20729255573	1.67985673767
6	4.12694974938	-1.95866931793	-0.815538227789	1.86854839643	0.933088723265	0.855868083128	-0.226623512332	-0.0942024161779	-0.386724767616	0.113593048027	0.0154219552676	0.56871796635	0.164787681349	-0.0203862086805	0.199209072149	0.344607829916	-0.0517326756577	0.0340985370177	0.239167992194	-0.0241171430139	0.459818287565	-6.98352382384	-9.85983804708	-5.2491450881
7	1.2589463493	-0.344356659156	-0.184433019462	1.36922329664	0.377877718832	1.23576194539	-0.0624891474759	0.231168889467	-0.173911868698	-0.139980798135	-0.185632846681	0.658482816968	-0.12358254248	-0.275061786521	0.231651374245	0.39279350556	-0.0204414929455	-0.0933062994738	0.389058365581	-0.0413248084126	0.518851903694	-13.5993905892	-1.59293110687	-10.6589317537
8	1.38464264132	0.0307778355189	0.0258793244416	0.756636891833	0.0621339738578	0.261086952922	-0.00294519032887	0.208251767565	-0.0129342662642	0.00671624015182	0.00514956323167	-0.19451740325	0.00908413869272	0.043296910653	0.00975896231935	0.333460875835	-0.0783473030773	0.0497930623961	0.397475914376	0.0318044955427	0.301973887105	140.272991854	51.9651717756	-38.2723956044
9	0.794992573674	1.46981189738	-0.891979930103	3.30996329021	-2.5297109314	2.23159063252	0.546435902739	0.75874081982	1.63699600966	-0.323312750508	-0.430138071166	-0.857042598744	-1.00757130686	0.0321427445993	-0.176663930525	1.29943980862	0.126078035125	0.297346014509	0.87536373823	0.547789121907	1.75239361747	113.721811849	98.6572278831	-35.621607112
10	1.62812541919	0.0085108314765	-0.199177698319	0.519175925376	-0.038410633019	0.33976470446	-0.0359411661525	0.0506243957588	0.343014654778	0.0293565199962	0.0512780636298	-0.0653236213071	-0.124200061041	0.0302251749824	-0.0155733411561	0.430997181469	-0.071170110185	0.0203786815541	0.397921600039	0.0398087453329	0.387770335223	137.105225865	71.3592897866	-31.6757466318
11	1.42321506228	-0.324646691004	-0.237607650395	1.37056659831	0.0176677047735	0.531547993368	7.32702861428E-5	-0.321921253861	0.292968747106	0.270432766764	-0.0718718916724	0.215775946609	-0.111605696826	-0.145601893972	0.0700202334557	0.457092426665	0.043403229117	0.0582678250102	0.563613371589	-0.224009721938	0.457323685481	72.0309639078	5.54797876999	-53.6375981193
12	1.93377564852	-0.26577474473	0.33376945912	0.646618971476	0.0261924066531	0.801371948771	0.0238749197247	-0.0916161553697	0.157574449438	0.0410333008059	-0.064746620578	0.130766794729	-0.0630211554976	-0.0591721610282	0.0297113700096	0.321708433923	0.0259264013983	0.00833480415291	0.278201861077	-0.0717882694484	0.340819629699	75.8187049323	-5.28366381076	-74.4353828263
13	3.99870825051	-0.640542234072	0.147410980982	2.38816132936	1.13969459063	8.10835395467	0.652422903371	0.867985651255	-0.706142895142	-0.954261334291	-0.33945216443	0.398383557659	0.620121857739	-0.193354582458	-0.364194483791	0.901835499537	0.244085281095	-0.162542041967	0.602633246668	-0.160520224297	0.675376595664	101.908012084	-32.026644329	-105.112622695
14	1.16852996108	-0.198524561025	0.542833990933	0.813959195171	-0.0613190601977	0.393698629012	0.0825045813634	0.0339444620705	-0.0684873453078	-0.0954776567621	-0.0752958170343	-0.108137654837	0.0454608603165	0.102491655056	-0.0312776305452	0.316376379261	0.0271570798631	0.0263902732722	0.36419707384	-0.0133411962205	0.362194368179	96.0654923474	-16.1370731688	-75.721793462
15	1.71755717051	-0.0517336884651	0.301568170422	1.5164173866	-0.438325403349	1.63024135419	0.100609278846	0.0386313612814	-0.133980139112	0.0341761647203	-0.0393959768732	0.234028105105	0.0392881792529	-0.00330912649016	-0.0801454173002	0.260655721116	0.0736507644757	0.0477154729835	0.302123232526	-0.0536930759146	0.328038954385	81.3306973147	-14.181941943	-79.8783180097
16	6.58673135561	-1.8056952505	-1.26348391027	2.04343652031	1.83044578519	1.95843753453	0.0916365625862	-0.10127859538	-0.565354541823	0.0767653152435	-0.0710099928305	0.19906002242	0.146667441364	-0.0274388584133	-0.0306103633017	0.393501360176	-0.0227149104803	-0.00393758989124	0.208037815205	-0.0161889976922	0.410183941583	66.6016900979	-22.8285785025	-81.7252982248
17	2.31426941142	-0.307241750026	0.193577498925	1.21241363613	-0.216763262195	1.05525319345	0.0916239774944	0.173525832621	-0.353526075162	-0.00593915722667	-0.0863416033786	0.207552361133	0.0685209893451	-0.0569637219777	-0.0110246405301	0.328340782165	0.0104061095801	-0.0401664070845	0.311687133135	-0.0578872116671	0.311107267333	64.9291460433	-17.7955362926	-87.3747737899
18	1.52668663171	-0.152875557651	-0.0456032719242	1.01850919076	0.420311261362	0.901701801889	0.10770354263	0.0161640227557	0.227358602208	-0.109582386188	0.0450957460699	-0.2789091709	-0.219524799186	0.170884383356	-0.145554494462	0.375487473923	-0.0541750713201	0.100924823527	0.393325724017	0.0156966133994	0.427686838411	11.6759773908	18.0825178712	-68.9792097828
19	1.58674055317	0.0766389167246	0.0874582327195	0.875916673248	0.016750717111	0.353196191664	0.077798180152	-0.15436123308	0.091497429004	-0.0118940262954	-0.0645258815345	-0.122774322228	-0.0248770933866	0.151615772124	-0.00671970943381	0.285792843158	0.0329005038309	0.044542135194	0.421761840961	-0.0428072431527	0.214117977068	10.7322896838	-4.60561970307	-66.3419020279
20	3.40340522819	1.10682474069	0.407127296527	0.441628309284	0.241502974279	1.05952725154	0.19279097344	-0.216622188572	-0.471032578415	0.0719693212797	-0.137597236515	-0.0946201787435	0.380802121497	0.0603824537698	-0.0369530603331	0.457107918222	0.0103651165474	-0.0177841548808	0.424369285294	0.048343214404	0.416514452219	-8.15103137366	-38.2141452337	-73.9075175197
21	5.99285344128	0.139842643176	-0.136915946764	6.51233180581	-0.0182284402201	6.54561676177	-0.198145131281	-0.170608725015	0.152264187654	0.658051677077	-0.39482690522	-1.37662794747	0.0027327613768	0.989992348912	0.584800024218	0.655837670085	-0.11580798243	-0.229722094637	0.5515217951	0.184028151733	0.940217895274	-8.83288803056	-48.2107137736	-69.9527127632
22	1.38350300598	0.257326385846	0.0852016019683	0.733828003249	0.128966485723	0.83544091609	0.0381981251514	0.113703766023	-0.0291469006822	-0.0452601582595	-0.0299768074412	0.15258428882	0.0520130505049	0.0163023767984	0.00170876985466	0.28053569013	0.0078160164425	0.0415895779603	0.424577361865	-0.0189357283125	0.278943434934	-8.23585445924	-14.2611649931	-75.8596177253
23	1.9517368215	-0.369643855963	-0.143948877214	1.59242560163	-0.24462488247	0.0475836164178	0.0788399111768	-0.0827055775275	-0.114149316132	-0.120730891216	0.0588063077277	-0.0742523421321	-0.00463144434882	0.228215868515	-0.157461592772	0.297290087389	0.000498749633093	0.0190126192944	0.439345492039	-0.0284062285254	0.256706945904	6.38705575883	-15.2061262831	-71.4050489951
24	4.06760043168	1.90898052314	0.705645837543	2.77229656705	0.83189381159	0.365644995694	0.0654497277882	0.152300483949	-0.0498169439911	-0.229047589319	-0.0309851175214	0.0236855714244	-0.00836088311734	0.290904835825	-0.0245693582917	0.390875766292	0.0970305890521	0.055992678727	0.481498575455	-0.0120814774697	0.262450732871	17.7486237238	-21.4257836676	-77.3228379761
25	1.71274805614	-0.10059567919	0.0744431551708	1.14510252692	0.174477032368	1.22538131295	0.0322291091101	-0.0922497459118	-0.224697654852	0.0038465365181	0.0795348287744	-0.218499569231	0.0151509376894	0.371550917281	-0.119833874125	0.324551042601	0.0801276967625	0.0247155545804	0.523627327559	0.0256223951634	0.30560891372	25.3598803622	-21.2602561642	-68.7866228969
26	1.5955966594	1.5844478907	0.226381509301	1.90102469549	0.711536732995	0.815341526706	0.131115543457	-0.140661911668	-0.59646820197	0.0165380387424	-0.0252638931308	-0.0926989307233	0.369988627845	0.0679543644383	-0.130654066554	0.564034133563	0.0655421307483	0.0563346656755	0.358611097678	0.215021518066	0.666487964041	14.7217783469	-118.851076064	-113.317385894
27	2.09127531813	-0.180634047324	-0.193478479899	0.636770535927	0.00583410894796	0.715426824536	-0.109129572361	-0.367555182942	-0.246478080526	0.0177637310385	-0.010995145008	0.0103919127554	0.100034036955	0.145640814258	0.0830856481373	0.359994425246	0.0280003616713	0.074735777505	0.308893734659	0.047291671718	0.266639480663	9.71903727089	-93.2627571382	-110.401460708
28	4.69992183818	-1.54368794505	-0.914927420021	6.98711092499	-0.283299304861	2.32357399921	0.321184850228	0.169617102737	1.23964357285	-0.937912074554	-0.177221672135	-0.049907748067	-0.907569625155	0.13433517835	-0.154012665519	1.08044310899	0.101319080045	-0.0711904954413	0.518170105398	-0.171061045616	0.756816862644	-7.05162472187	-46.3405626347	-110.017352575
29	1.48136041331	0.320214624204	-0.147236000493	0.394589831036	0.163644904807	1.04604150846	-0.0448219354768	-0.357662928436	0.204891120382	-0.0491665525735	-0.122211862364	0.198173208785	-0.227751607571	-0.173874650373	0.110575896563	0.392204181473	0.105371595814	-0.00305518966898	0.389588000657	-0.0341083605017	0.426629551215	-8.64540508019	-78.9281613702	-105.284453532
30	2.08803984496	-0.095139594989	-0.144095329356	1.67467207171	-0.603518156873	1.20842704054	-0.0847449874931	-0.536459367819	0.0617294759021	0.114645352293	0.105633554269	-0.0132131150521	0.0198897609573	0.193706747802	-0.0392884388721	0.27859048036	0.0577626964902	0.040835353381	0.345416937468	-0.0173138991228	0.292957015347	6.57212376432	-81.1730922819	-107.944890204
31	2.7427820956	-0.714484534832	0.779431696449	6.75141865409	0.690690448834	2.84186544409	-0.129904419619	-0.894173230025	0.199898361815	0.730987305514	0.0893826538587	0.115317487448	-0.144499744751	0.288658551306	0.0668265863798	0.36851492879	-0.0285972487573	0.00294043719178	0.617484620396	-0.0230610714703	0.321044965246	23.5152253469	-78.9549104238	-100.211078663
32	2.49085808498	-0.443137573452	-0.473410361048	1.35379144675	0.329409040366	1.884347151	-0.0873808481546	-0.513070332002	0.404123145316	0.0870517690174	0.0116076639417	-0.176880663479	-0.0947737610984	0.374120191429	0.0859658612097	0.372690613543	-0.0578249891938	-0.0111479324586	0.430363278127	0.0117713226963	0.32017831039	23.8067119331	-75.5385511664	-108.339304098
33	0.991336134956	-0.673618923954	0.435421944494	2.25508241469	1.50845715455	1.40979134021	-0.12957605509	0.302238345414	0.463180925991	-0.291944835722	0.175903545421	0.0503293307569	-0.362389200265	0.189356055449	-0.0591220150634	0.617000545972	-0.189591813687	-0.074303638396	0.428365280547	0.159418710419	0.589886561015	-55.6441703243	22.3501278798	15.8972837321
34	0.856557943736	-0.2422226276	0.621039409502	1.11925646951	0.230953771349	1.29246323809	-0.291180664495	0.438164093265	0.328124227399	-0.193669807358	0.0935439884659	-0.0398096431733	-0.525541866055	0.532609701315	0.156904901502	0.560265921884	-0.206314432753	-0.107978835036	0.530427334604	0.158689230582	0.440450107099	-57.8827049346	10.0146344282	7.3870963961
35	2.20460458858	0.671532746099	-0.630973355135	0.705292576515	-0.0606370070684	1.36903027297	-0.0884377323213	0.066731682734	0.123016781112	-0.00676797188467	0.0702714899982	0.0250008222235	-0.0049654228144	0.327067543193	0.026866227956	0.374987213289	0.0379845721676	0.00278122036441	0.292890643164	0.0426995485763	0.232127603699	-70.1447441153	-8.83858327188	15.8989946919
36	2.95255178574	0.671168369332	0.0337664176195	0.631663529558	-0.853670953198	1.30896285655	0.0283509280126	0.212843342812	-0.1853889257	-0.247509415639	0.160015666791	0.064639459569	0.263648377647	0.040297118874	-0.166629819785	0.526078879156	0.0645826308329	0.0252531035575	0.26203716018	0.00823152861731	0.337019150981	-90.3984858049	-27.0197052884	10.775475447
37	3.02241935063	1.01697841024	0.282963097959	0.836824849766	0.22422590294	0.718795755636	-0.15048362062	0.0927767988889	-0.131852238804	-0.203941128833	0.0365166783896	0.0957660449961	0.219284725779	-0.0275826062295	0.119261396265	0.512728666586	0.0574163881206	0.0680107402508	0.302791250881	0.0498534241679	0.284007364565	-94.1687506054	-31.0842666828	8.40472928415
38	2.09861971585	-1.07111079906	1.69249873932	1.55458085321	-0.733619297787	2.68719402879	-0.362274074875	0.235206101188	0.201826555306	0.028836772219	0.0354455761978	-0.0362033132936	-0.316778692781	0.055566769218	0.289917342051	0.37242743316	-0.0891393488374	-0.041375207818	0.298923983912	0.088219574458	0.307902455447	-79.72529373	2.17573332656	2.64258046396
39	1.37935729825	0.509774345404	0.834616436621	0.640099379081	0.41700355244	1.52335823323	-0.0202755724212	0.509255225249	-0.27776088233	0.0522165756645	0.225258327315	-0.21358517807	0.277831503038	0.630395907314	-0.172086412205	0.470164666053	0.155026334912	0.0271231511939	0.54214534015	-0.0367049229666	0.336955180734	-58.7491783867	-21.1878512849	10.8178076255
40	2.10828627195	0.222860308223	0.632033275644	1.1913550818	0.105763726017	0.83462010223	-0.171996107986	0.203833989917	0.00750288505489	-0.410360932131	0.083773842914	0.207569831956	-0.0988840217883	0.0336154318023	0.0852142775849	0.52177299841	-0.00567415461251	-0.0641705816482	0.303641178452	-0.0897259187002	0.36729685464	70.166084464	-95.284550215	-130.81478407
41	0.981064949852	0.31355245327	0.285483669435	0.744426966343	0.103167964319	0.517443527911	-0.115618197373	-0.198538188118	0.20849444946	-0.0752176787091	-0.0476580292228	0.16405108114	-0.119645968975	-0.0384190568521	0.176131017149	0.353896060899	0.0662967944229	0.0104556955264	0.307110302034	-0.0800708811309	0.373334196845	80.2743542705	-83.6440412011	-103.444912685
42	1.18012124188	0.420361378297	0.206397351298	1.12989217107	0.306426123054	0.513190190244	-0.0898471081606	-0.234884867258	0.208045088597	0.124088313865	-0.00118357582983	-0.0611059780868	-0.0901360437517	0.0362483543865	0.0724817641713	0.422620569983	0.0603728594565	-0.0660181754305	0.38904913483	-0.0255523692505	0.456568380755	96.4073472134	-73.5962973387	-101.385132107
43	1.56218792122	0.178972991914	0.347412744078	1.01883861065	0.0248127480178	0.560390983671	-0.205369169392	-0.452107506775	0.610839505099	-0.0672727521108	-0.0865674109864	0.341266387666	-0.225820435167	-0.225053622695	0.218873943601	0.47542418963	0.133007860884	-0.0738058880265	0.463090875008	-0.240706560187	0.672921391455	67.687091205	-72.7095391111	-101.380172569
44	1.79953928022	0.199450260772	0.57033851095	1.16779074304	0.230954846769	0.619002112518	0.0913400827878	0.365218900161	-0.326598231274	-0.163119821364	-0.0931277666039	0.0956596284311	0.060705505347	-0.0293824667848	0.0101912689218	0.4477126495	-0.0226833758002	0.0469330913056	0.523832722931	-0.207149538851	0.412925759215	69.4367440687	40.902937852	-55.2808701978
45	1.73676519621	0.0148062616219	0.293878443952	0.488717535283	-0.0489891643612	0.707532198504	-0.0408260442723	0.104696922339	-0.257033917787	-0.0338634572172	-0.0020474279851	0.0700199800176	0.114393299743	-0.0468236386768	0.0354240633735	0.324659397089	-0.00923382763026	0.113155669373	0.265401668223	-0.075157546403	0.331214875311	70.2633338963	50.4999376476	-34.5079839643
46	1.08999148073	-0.0778096983337	1.92465603156	0.589427317061	-0.0273208460655	5.01450302264	-0.105628126014	0.0963162446714	0.107689468546	-0.00760419124175	0.0511928671837	-0.115508841431	-0.497234969245	0.0988541534292	0.0369828025014	0.425942660373	-0.0301843698731	0.056242201589	0.332355427564	0.0221006521832	0.31233447153	90.4441840523	72.6764059346	-4.12863129973
47	1.19733831458	-0.227440150688	-0.0219002458592	0.263334650788	0.228000550902	0.921547114133	-0.067023063943	0.106499331602	-0.0425312132283	-0.0678784437166	0.0152206992176	-0.0975896691553	-0.138033417563	0.196644807894	0.0437215240566	0.429152339541	-0.0557889038768	0.0643971197295	0.373399638374	0.0162949689948	0.367734048225	89.5051463736	64.0765161382	-31.5682997377
48	1.68369124825	-0.371112517176	0.0748287550211	0.374474941986	0.389934933815	1.47778845202	-0.0251108868648	0.0328287609761	0.02604370534	0.0321213473858	0.0329482163198	0.217907669287	-0.042110890684	-0.0688964425873	-0.00130226801326	0.368344889704	-0.0471929053556	0.0729643214001	0.306093304045	-0.0056475904497	0.392427661287	74.6322080706	60.5077048719	-28.2088909048
49	6.63358105075	2.76418567654	1.48820222237	2.8765948031	1.47672302938	1.09819761155	-0.15960994616	0.199522246574	0.222449719988	-0.150117171415	0.0732153989565	0.254807679208	-0.31240301539	-0.0147323255403	0.0775508699238	0.391998990531	0.0460702972558	0.0512236816865	0.263480243745	-0.0313453340366	0.25348210622	63.0935859126	68.7947666798	-26.178354702
50	1.5217076906	0.0100018031871	-0.141771378027	0.889296448433	-0.00865095718896	1.10710292722	-0.0975116166514	-0.128519778286	-0.0648144024298	0.0384624043783	-0.0291982275353	0.245152059131	0.0856196198596	-0.0815794065426	0.115680968761	0.338300511768	0.0107137465659	0.089970606074	0.329209662681	-0.0430741265669	0.322113860615	56.1458833102	61.9831057011	-21.1168465141

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 1 through 132 )	A	A	1 - 132	1 - 127
2	2	chain 'A' and (resid 133 through 362 )	A	A	133 - 362	128 - 357
3	3	chain 'A' and (resid 363 through 458 )	A	A	363 - 458	358 - 453
4	4	chain 'A' and (resid 459 through 574 )	A	A	459 - 574	454 - 569
5	5	chain 'A' and (resid 575 through 819 )	A	A	575 - 819	570 - 814
6	6	chain 'A' and (resid 820 through 914 )	A	A	820 - 914	815 - 909
7	7	chain 'A' and (resid 915 through 1131 )	A	A	915 - 1131	910 - 1126
8	8	chain 'B' and (resid 2 through 483 )	B	D	2 - 483	1 - 477
9	9	chain 'B' and (resid 484 through 561 )	B	D	484 - 561	478 - 555
10	10	chain 'B' and (resid 562 through 1131 )	B	D	562 - 1131	556 - 1125
11	11	chain 'C' and (resid 1 through 132 )	C	G	1 - 132	1 - 126
12	12	chain 'C' and (resid 133 through 483 )	C	G	133 - 483	127 - 477
13	13	chain 'C' and (resid 484 through 574 )	C	G	484 - 574	478 - 568
14	14	chain 'C' and (resid 575 through 754 )	C	G	575 - 754	569 - 748
15	15	chain 'C' and (resid 755 through 825 )	C	G	755 - 825	749 - 819
16	16	chain 'C' and (resid 826 through 894 )	C	G	826 - 894	820 - 888
17	17	chain 'C' and (resid 895 through 1131 )	C	G	895 - 1131	889 - 1125
18	18	chain 'D' and (resid 1 through 132 )	D	J	1 - 132	1 - 125
19	19	chain 'D' and (resid 133 through 467 )	D	J	133 - 467	126 - 460
20	20	chain 'D' and (resid 468 through 521 )	D	J	468 - 521	461 - 514
21	21	chain 'D' and (resid 522 through 574 )	D	J	522 - 574	515 - 567
22	22	chain 'D' and (resid 575 through 754 )	D	J	575 - 754	568 - 747
23	23	chain 'D' and (resid 755 through 825 )	D	J	755 - 825	748 - 818
24	24	chain 'D' and (resid 826 through 914 )	D	J	826 - 914	819 - 907
25	25	chain 'D' and (resid 915 through 1131 )	D	J	915 - 1131	908 - 1124
26	26	chain 'E' and (resid 2 through 90 )	E	L	2 - 90	1 - 79
27	27	chain 'E' and (resid 91 through 483 )	E	L	91 - 483	80 - 472
28	28	chain 'E' and (resid 484 through 561 )	E	L	484 - 561	473 - 550
29	29	chain 'E' and (resid 562 through 754 )	E	L	562 - 754	551 - 743
30	30	chain 'E' and (resid 755 through 825 )	E	L	755 - 825	744 - 814
31	31	chain 'E' and (resid 826 through 880 )	E	L	826 - 880	815 - 869
32	32	chain 'E' and (resid 881 through 1131 )	E	L	881 - 1131	870 - 1120
33	33	chain 'F' and (resid 1 through 89 )	F	N	1 - 89	1 - 82
34	34	chain 'F' and (resid 90 through 262 )	F	N	90 - 262	83 - 255
35	35	chain 'F' and (resid 263 through 439 )	F	N	263 - 439	256 - 432
36	36	chain 'F' and (resid 440 through 521 )	F	N	440 - 521	433 - 514
37	37	chain 'F' and (resid 522 through 649 )	F	N	522 - 649	515 - 642
38	38	chain 'F' and (resid 650 through 774 )	F	N	650 - 774	643 - 767
39	39	chain 'F' and (resid 775 through 1131 )	F	N	775 - 1131	768 - 1117
40	40	chain 'G' and (resid 1 through 189 )	G	Q	1 - 189	1 - 182
41	41	chain 'G' and (resid 190 through 521 )	G	Q	190 - 521	183 - 514
42	42	chain 'G' and (resid 522 through 754 )	G	Q	522 - 754	515 - 747
43	43	chain 'G' and (resid 755 through 1131 )	G	Q	755 - 1131	748 - 1115
44	44	chain 'H' and (resid 1 through 132 )	H	T	1 - 132	1 - 126
45	45	chain 'H' and (resid 133 through 467 )	H	T	133 - 467	127 - 461
46	46	chain 'H' and (resid 468 through 574 )	H	T	468 - 574	462 - 568
47	47	chain 'H' and (resid 575 through 754 )	H	T	575 - 754	569 - 748
48	48	chain 'H' and (resid 755 through 825 )	H	T	755 - 825	749 - 819
49	49	chain 'H' and (resid 826 through 913 )	H	T	826 - 913	820 - 907
50	50	chain 'H' and (resid 914 through 1131 )	H	T	914 - 1131	908 - 1122

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi