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- PDB-8s3d: Crystal structure of Medicago truncatula glutamate dehydrogenase ... -

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Open data

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Basic information

Entry

Database: PDB / ID: 8s3d

Title

Crystal structure of Medicago truncatula glutamate dehydrogenase 2 in complex with 2-amino-2-hydroxyglutarate (reaction intermediate) and NAD

Components

Glutamate dehydrogenase

Keywords

OXIDOREDUCTASE / complex with reaction intermediate / glutamate dehydrogenase

Function / homology

Function and homology information

glutamate dehydrogenase (NAD+) activity / L-glutamate catabolic process / nucleotide binding / mitochondrion / metal ion binding
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Grzechowiak, M. / Ruszkowski, M.

Funding support

Poland, 1items

Citation

Journal: Int.J.Biol.Macromol. / Year: 2024
Title: Legume-type glutamate dehydrogenase: Structure, activity, and inhibition studies.
Authors: Grzechowiak, M. / Sliwiak, J. / Link, A. / Ruszkowski, M.

History

Deposition	Feb 19, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 4, 2024	Provider: repository / Type: Initial release

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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	8s3d.cif.gz	1021.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8s3d.ent.gz	834.6 KB	Display	PDB format
PDBx/mmJSON format	8s3d.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/s3/8s3d ftp://data.pdbj.org/pub/pdb/validation_reports/s3/8s3d	HTTPS FTP

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Related structure data

Related structure data	8s38C 8s39C 8s3aC 8s3bC 8s3cC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.18150/STKHH7 / Data set type: diffraction image data / Metadata reference: 10.18150/STKHH7

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

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Assembly

Deposited unit

A: Glutamate dehydrogenase

B: Glutamate dehydrogenase

C: Glutamate dehydrogenase

D: Glutamate dehydrogenase

E: Glutamate dehydrogenase

F: Glutamate dehydrogenase

hetero molecules

279 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	111.832, 155.707, 163.089
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	Glutamate dehydrogenase Mass: 44894.016 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: 11433210, MTR_5g013470, MtrunA17_Chr5g0399821 / Production host: Escherichia coli (E. coli) / References: UniProt: G7JYL4

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Non-polymers , 10 types, 2706 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-8GL / (2S)-2-azanyl-2-oxidanyl-pentanedioic acid Mass: 163.129 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₅H₉NO₅ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#7: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#9: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#10: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#11: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2636 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.65 Å³/Da / Density % sol: 53.55 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Amino acids (0.02M DL-Glutamic acid monohydrate; 0.02M DL-Alanine; 0.02M Glycine; 0.02M DL-Lysine monohydrochloride; 0.02M DL-Serine ) 0.1M Imidazole/MES monohydrate pH 6.5 20% v/v PEG ...Details: 0.1M Amino acids (0.02M DL-Glutamic acid monohydrate; 0.02M DL-Alanine; 0.02M Glycine; 0.02M DL-Lysine monohydrochloride; 0.02M DL-Serine ) 0.1M Imidazole/MES monohydrate pH 6.5 20% v/v PEG 500* MME; 10 % w/v PEG 20000

Crystal

Density Matthews: 2.65 Å³/Da / Density % sol: 53.55 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Amino acids (0.02M DL-Glutamic acid monohydrate; 0.02M DL-Alanine; 0.02M Glycine; 0.02M DL-Lysine monohydrochloride; 0.02M DL-Serine ) 0.1M Imidazole/MES monohydrate pH 6.5 20% v/v PEG ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 1.65→65.89 Å / Num. obs: 337626 / % possible obs: 99.5 % / Redundancy: 7.49 % / B_iso Wilson estimate: 20.18 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.092 / Net I/σ(I): 6.83
Reflection shell	Resolution: 1.65→1.75 Å / Redundancy: 7.56 % / R_merge(I) obs: 1.445 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 53784 / CC_1/2: 0.532 / R_rim(I) all: 1.548 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
PHENIX	1.18.1_3865	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→65.89 Å / SU ML: 0.1779 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.6097
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1735	3376	1 %
R_work	0.1468	334188	-
obs	0.1471	337564	99.5 %

Solvent computation

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

Displacement parameters

B_iso mean: 24.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→65.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18834	0	616	2636	22086

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0118	20104
X-RAY DIFFRACTION	f_angle_d	1.1525	27200
X-RAY DIFFRACTION	f_chiral_restr	0.0647	3000
X-RAY DIFFRACTION	f_plane_restr	0.0085	3544
X-RAY DIFFRACTION	f_dihedral_angle_d	17.4799	7537

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 (%)
1.65-1.67	0.2804	137	0.2791	13494	X-RAY DIFFRACTION	97.34
1.67-1.7	0.3204	139	0.2629	13801	X-RAY DIFFRACTION	99.21
1.7-1.73	0.2573	139	0.2469	13733	X-RAY DIFFRACTION	99.11
1.73-1.75	0.2637	139	0.2308	13798	X-RAY DIFFRACTION	99.2
1.75-1.78	0.2353	140	0.2232	13805	X-RAY DIFFRACTION	99.31
1.78-1.82	0.2487	139	0.2148	13766	X-RAY DIFFRACTION	99.2
1.82-1.85	0.2345	139	0.2032	13823	X-RAY DIFFRACTION	99.33
1.85-1.89	0.244	140	0.1971	13815	X-RAY DIFFRACTION	99.46
1.89-1.93	0.2297	139	0.1887	13825	X-RAY DIFFRACTION	99.39
1.93-1.98	0.1992	140	0.176	13869	X-RAY DIFFRACTION	99.43
1.98-2.03	0.2168	140	0.1607	13817	X-RAY DIFFRACTION	99.54
2.03-2.08	0.1927	141	0.147	13929	X-RAY DIFFRACTION	99.6
2.08-2.14	0.1727	140	0.1405	13853	X-RAY DIFFRACTION	99.65
2.14-2.21	0.1641	140	0.1369	13925	X-RAY DIFFRACTION	99.69
2.21-2.29	0.1777	141	0.1319	13942	X-RAY DIFFRACTION	99.75
2.29-2.38	0.1915	141	0.1292	13960	X-RAY DIFFRACTION	99.82
2.38-2.49	0.1741	141	0.1288	13961	X-RAY DIFFRACTION	99.82
2.49-2.62	0.1497	141	0.1239	13957	X-RAY DIFFRACTION	99.85
2.62-2.78	0.1527	142	0.1242	14038	X-RAY DIFFRACTION	99.85
2.78-3	0.154	142	0.1271	14044	X-RAY DIFFRACTION	99.89
3-3.3	0.1749	142	0.1347	14067	X-RAY DIFFRACTION	99.96
3.3-3.78	0.1245	143	0.1268	14120	X-RAY DIFFRACTION	99.97
3.78-4.76	0.1412	144	0.1136	14250	X-RAY DIFFRACTION	99.97
4.76-65.89	0.1591	147	0.1615	14596	X-RAY DIFFRACTION	99.54

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.22619071516	-0.371801555205	-0.203860899543	0.726343500965	0.0517267256607	0.359635260163	0.0651468000572	0.133312093974	0.0194154780872	-0.0651782294104	-0.0321154345347	0.0691897206904	-0.0124120547181	-0.0816770085201	-0.0324929125758	0.165599254327	-0.00102661208508	0.00206448945368	0.178273559755	0.0149216851043	0.148735624975	3.02028797581	23.1650793282	38.4323124702
2	1.54134246012	-0.504043962897	-0.582519526842	1.16540899563	0.699753377379	1.44486704745	0.00328255239211	-0.0645542422671	0.144564363825	-0.016582676471	0.0697997533284	-0.0710553609864	-0.0839856485721	0.12646503005	-0.0795003767324	0.132652215806	-0.0127414791947	-0.0139365061844	0.172572655519	-0.00938157755938	0.165791297069	17.5169782405	20.8565569504	47.5543052107
3	0.800409417374	-0.383375923402	-0.343890381216	3.10620668102	0.336916598812	1.01865401389	-0.054194415858	-0.105305422143	-0.0310581118313	0.283056762291	-0.0136079572224	0.22861685511	0.0203986198823	-0.111548478406	0.0690308867287	0.1629297652	-0.00523046364848	0.0190106168135	0.182524001384	-0.0007191552913	0.130833963461	-7.47456359824	15.0204496407	60.8590998608
4	2.75964675733	0.0180388525303	0.632045219167	5.06590537935	0.569062907811	5.04504377708	-0.0135817750188	-0.162939901903	-0.285000395449	0.192157101938	-0.0185416328121	-0.0343991739376	0.205998223916	-0.0195148158334	0.0378663668235	0.167372591437	-0.0148987923054	0.026380270198	0.114445104441	0.0357960193812	0.177279542799	-3.72475184219	-0.828641230121	58.4727832037
5	3.73202879106	0.300796853411	0.375992832678	4.04000292858	-0.695454170622	3.71548416231	-0.0388200562074	0.189594886306	-0.271484019793	-0.0878660416644	0.00617092371487	0.41355402664	0.227671374378	-0.265586156469	0.0266699796311	0.112514107609	-0.0291753874408	0.00893504323092	0.150177580677	-0.0222825246713	0.200820395549	-14.4536997541	8.43462478166	48.2060625765
6	5.77042726893	1.97747427568	1.78623645804	2.18833607649	0.837235801048	1.75008385709	-0.0760640655879	-0.0888722288296	0.226383784734	-0.000941429293959	-0.00242041470752	0.0906324249554	-0.0646632446909	-0.035536638073	0.0975772985765	0.123168928007	0.0155361249891	0.0118901325208	0.0990599995484	0.0133570293355	0.122795887918	-3.35394029053	23.2549004736	51.9682794584
7	7.95305052766	-4.12851625516	5.35963522395	4.48271427758	-2.31776215076	6.27123720922	-0.148909634044	-0.461993407971	0.289605486817	0.248865207845	0.1234153995	0.00564439810109	-0.229636125405	-0.291048700285	0.0512358831352	0.161043822722	-0.0007620891539	0.0578094305195	0.175346301317	-0.0198313805578	0.164759759645	-7.22102393583	30.2697911053	59.84569518
8	3.18225507931	3.48833082419	-2.19516757225	3.8351567047	-2.27759944891	2.28607384897	0.192440360749	0.0443528561245	0.162368637966	0.148134559853	-0.0376434306608	0.211106009448	-0.159530942305	-0.0738568823933	-0.1806643282	0.143720372141	0.040687180326	0.0115994642619	0.177929173136	0.0232108825847	0.203580895836	-7.14278472592	37.1480563576	43.2156180512
9	1.32955009677	-0.011822981839	1.22228779994	0.781591449456	-0.677811351956	3.43688555947	0.0673029141061	0.0467745262494	0.167202835523	-0.0159784184893	0.0630660804676	0.129144654262	-0.174701296572	-0.168275298005	-0.108228454506	0.178751869135	0.0446359826335	0.0577159172543	0.174120514958	0.00310554901654	0.237442411953	26.0929880873	68.5578181685	27.2491047098
10	0.686118859942	0.0631012238551	0.611632202652	0.482611392685	0.232784385238	1.23802253807	0.031991986173	-0.0715965076354	0.0582322249299	0.0349180918869	-0.00845827986944	0.00287465355356	-0.109501831644	-0.0501011411862	-0.0155727847245	0.176744662845	-0.0111788974399	0.0316426120343	0.164503231607	-0.00341353551807	0.188168693057	37.7643452224	63.3402618853	34.0458970803
11	0.470955793982	-0.166131592448	0.277978931446	0.49013297941	-0.0852519044241	2.14827733973	0.0751739800127	-0.00858435054319	-0.0374738011168	0.0373148941877	-0.00271877253749	0.030357625779	0.046212535119	0.0685936363846	-0.060510514229	0.15549829876	-0.00136571603925	0.00115239205092	0.147268999691	-0.0176072897524	0.191498447575	44.7573993124	55.53348256	31.8002621375
12	2.23847745089	0.0471445908277	0.00415913659385	2.27133571283	0.172566636113	2.40156553107	0.109393268525	-0.0700245184655	0.212103774447	0.064825220162	-0.0272531185722	-0.214095332415	-0.18459921991	0.297337344246	-0.0725217784408	0.184684093448	-0.0515109140558	0.0452085430863	0.204060296898	-0.0334894161449	0.219249068943	58.4551056467	75.1023066252	21.0375918332
13	2.88782850109	-0.379300269828	1.30813933899	4.89752525827	-0.497044138375	3.72139622308	-0.102781878975	-0.0115463358225	0.513973203673	0.142796565198	0.0305955766933	0.000595805340968	-0.619210011124	0.124757791036	0.0182370125155	0.239117614151	-0.0376190208273	0.0364860742979	0.138776524134	-0.0048756782671	0.258886332457	43.9847419615	82.3287569445	20.3211469148
14	1.86476983057	0.642044267885	-0.345792185798	2.89736277449	-0.118406682209	2.67600121424	0.0599014208428	0.0917688160034	0.298041141897	0.0627084230679	0.0347245635028	0.214763459783	-0.311407605973	-0.0804684524007	-0.0964234271778	0.183022581399	-0.00826995152256	0.0283731351857	0.134927858336	0.0146955140687	0.198661097669	39.1089222971	76.5432932883	17.3968539777
15	3.03323262013	0.931406054811	-1.0578596949	2.74846215848	-1.41826880825	3.46891679676	0.151644775166	0.127523462152	-0.417594393534	0.0779050882437	0.0941658640374	-0.107223106594	0.444050785615	0.12543305459	-0.195057525522	0.169221442964	0.0206345365805	-0.0693062319746	0.14718813287	-0.0536227924405	0.183558329142	44.9846004255	47.8428121289	21.5131443476
16	4.13607748915	-4.90668257043	2.93514088739	6.49164402714	-2.78951468701	3.20542992909	0.353959555788	0.603894408267	-0.172549070349	-0.53254346892	-0.17326378433	0.091145365391	0.234316954668	0.269915324696	-0.132543479036	0.216929016628	0.0104041362341	0.0149295085455	0.273861902023	-0.0269564287835	0.186219990368	41.4525629134	59.5875039018	9.08489915028
17	3.90130623452	2.94730219139	-1.36716574387	3.15316265162	-0.881333275704	0.931861977537	-0.0220494784397	0.248125870921	0.0958519435827	-0.0719156312189	0.104259548298	0.0525686789948	-0.0790198322516	-0.0620719228474	-0.0967376107072	0.172847309867	0.0225293885553	-0.00341035952952	0.188403925557	0.0334870256103	0.171080553761	25.2475550074	62.5178266894	15.8007977784
18	1.99999603149	2.00001615409	1.99998653191	2.00000796045	1.99997019651	2.00000709662	2.82622744537	3.37651925627	6.2599652269	-3.50193247163	-2.25453465514	-5.87943956917	-3.09849182459	-2.1775591131	-0.565811664184	0.437993116786	0.0106962877855	0.172328470727	0.789948371724	0.367885645553	0.5910798758	49.9372943789	59.4244981504	28.7556412447
19	0.965922897318	0.476469542897	-0.0483672879388	0.996748136398	-0.0661943549611	0.286721552056	0.0608464736874	-0.148374929584	0.0644778295092	0.0690755394155	-0.0757292662751	-0.0180034205086	0.0164857425041	0.0864587721622	0.0160025632644	0.160546884438	-0.000794740521418	-0.00255794726142	0.197839360104	-0.0121685447258	0.167464909949	53.4258491044	25.4282157915	43.411476009
20	2.22428862162	0.713340405001	-0.609560871121	0.677908445795	-0.273733948015	0.633128723957	-0.0583851350447	0.0708117960335	0.156332948724	-0.0555674976695	0.0330482496706	0.0911758340581	-0.016085849577	-0.0487103219336	0.0168798436865	0.141961447651	0.00428179679877	-0.0231782608358	0.139381282804	0.00340118329727	0.157553437524	44.6941303316	21.7280862077	31.1253789242
21	1.76780730077	-0.229762681014	0.0567875292705	3.23015380283	-0.141882267124	2.06673668766	-0.0227080482239	0.177840778469	-0.210947573697	-0.307507372451	0.0165927065261	-0.159780088706	0.128004986564	0.0684610889666	0.0343845185301	0.168964370291	0.0125219834219	0.0363450616918	0.158782636744	-0.0188786864268	0.14915557465	63.5406204876	6.13261363604	23.4146790328
22	3.57490825162	0.224407516982	0.136960497201	3.55456087536	0.111127009576	1.96961722543	-0.0467884795369	-0.114731945279	-0.213377623193	0.137646068938	-0.0122961287312	-0.489590292371	0.183943694586	0.256292684495	0.045319957101	0.123090321051	0.0292845155878	-0.00695792095666	0.171453767151	0.0311946337261	0.212061817315	71.8651647351	11.8176540515	34.8824638406
23	5.77245568576	-0.921852983199	1.93375969273	2.55155051442	-0.83992721012	1.98355242244	-0.0938367462982	0.11208962111	0.22843488079	-0.163557749768	0.0259563589448	0.0527562252193	-0.0136175043408	0.0558640496878	0.0674620812577	0.127063332476	-0.00625949351126	0.00801083394649	0.106422321523	0.00028051081588	0.107045088406	59.9549497085	25.4957348411	30.0163967132
24	5.20423834933	1.53874879057	3.35208259714	2.54469334231	0.498510090609	6.04940340647	-0.256035276298	0.445899471878	0.320801495015	-0.355743836468	0.183504988385	0.067206121341	-0.140045946071	0.121639467279	0.0887319880582	0.188277357828	-0.0241847146224	0.01891830638	0.182044527753	0.0512963175796	0.129575032383	63.3798607614	32.4519753073	21.9449522003
25	2.79940969837	-3.38649354031	-1.88904679502	4.06597005578	2.19126236797	2.16120059789	0.0890088926353	-0.0545074545674	0.0367945379021	-0.0760304242739	-0.0702371338415	-0.136699167974	-0.065207803149	0.0944771183051	-0.0285246243558	0.128862923966	-0.0375500308466	-0.00877851709803	0.174258177851	0.00430816085055	0.187615041239	62.2870367798	40.1844528384	38.2559715252
26	1.99999012689	9.45222775053	1.99999848331	2.00001158326	1.0598322234	1.99998613615	-0.251388034563	0.905346627554	-4.25413354349	-0.321465474591	3.54874630925	-4.97982657299	-1.82810888142	4.31430467962	-3.33801882573	0.477871518501	-0.0884707430605	0.267083105951	0.506436603038	-0.306410782883	0.984096960681	49.1266648295	17.768507034	27.472960401
27	0.538141446325	0.147092147417	0.100761196919	0.533653426778	-0.0616445267942	0.832605452654	0.0748430291309	0.0355167508379	0.0612673728172	0.0425003418585	0.0302499496986	0.0355154499738	-0.156121935596	0.0665726108747	-0.0909530908137	0.194579729502	-0.00164086080847	0.0553941264722	0.169301986105	-0.00662857059055	0.199581887341	17.3368371469	61.0886577557	46.9484332257
28	1.06923812171	0.107774569648	-0.488053722479	0.604799557413	-0.0680991931105	1.26840834047	0.210501707171	0.0105097103363	0.263873295555	0.0792967902668	0.0146973907167	0.152050880345	-0.382869145381	-0.243842283577	-0.104111627108	0.304910848512	0.0517203543966	0.100731293739	0.187443271126	0.0321673308841	0.244268355483	6.54607178485	66.961919005	62.0677014002
29	2.4627939902	-2.85229796434	-0.6613646993	4.26221406301	1.44511372222	1.30984790419	-0.0378173255532	0.014273294226	-0.124320754861	0.105258767453	0.111121388565	0.025435999592	0.163580477516	-0.0300244319634	-0.0686020451183	0.142606303876	-0.0562768213317	0.0259876692206	0.13638644628	0.0313475235613	0.152694079272	14.6682392691	16.8388989332	19.764910424
30	1.28817832861	-1.06139978057	-0.393034587774	1.32261387632	0.34490530678	0.360627054416	-0.0195829690746	0.0475587341659	-0.0108641054765	0.00106185822777	0.00515468410312	0.0964265135403	-0.0229443211621	-0.077671530709	0.0205846432076	0.174820802263	-0.0060946069541	-0.00804172977948	0.197295461034	0.00813038695184	0.159333374229	13.3424144491	30.5511695353	18.3171549044
31	2.49173022832	-0.408670569942	-0.931443900665	1.02006095676	0.494706467871	1.50542210224	0.0514924442398	-0.119167351517	0.100920920759	0.0524837740078	0.026183823142	-0.0577539768267	-0.0160643217922	0.0297862879073	-0.0835719188869	0.139916213679	-0.0112873038728	-0.0161539071152	0.123258849855	-4.17668124864E-5	0.141998925844	18.7454154383	41.4540455416	20.6986117865
32	1.95318320083	-0.709519670166	0.816290593652	1.39889114049	-0.688587770049	1.36190934334	0.0105387999942	0.185281993572	0.106621354633	-0.150041443501	-0.0478156768112	-0.0243506167982	-0.0817610239127	-0.00729578782926	0.0381249665147	0.204898892148	-0.00242936919479	-0.00668808248564	0.226671894505	0.00998375035067	0.156193816608	15.5485706234	35.1381298496	-7.47518459511
33	1.87731703962	-0.847026049141	0.499225904215	2.49222881947	0.238224780683	2.58321881634	0.106935098798	0.179210642394	-0.20688342343	-0.224721458157	-0.0620651789467	0.272306321722	0.154808236	-0.219036842024	-0.0550826193591	0.177669774289	-0.0111960503874	-0.0489449629495	0.21084903725	-0.0214029736311	0.164706458857	8.70657356775	22.9637901089	-5.10333590393
34	3.50056365728	2.79508417538	2.13380500429	4.23387335624	2.35423582161	2.29146195523	0.0671640495471	0.0264831461257	-0.111784630676	-0.0172060801065	-0.00621453492422	-0.164153756105	0.0334453500781	-0.012502682161	-0.0737296464947	0.11286954974	0.0112639769923	-0.0094154508637	0.131716863405	0.0139073698517	0.0964431224263	22.9330065842	26.9490373074	7.02550456543
35	3.78427961355	3.00940385887	0.0673533636259	2.65608047576	0.658374584299	1.42791073268	-0.0706039600707	0.101678668782	-0.106063976221	-0.235554758586	0.0864945712181	-0.453937965297	-0.00282816243789	0.184501095808	-0.0389598084544	0.181105012624	0.0118928500258	0.00574200940485	0.24197465917	0.00219892096407	0.14936718847	33.0772585851	24.3834360383	3.34275362951
36	1.80079194353	-0.086444653899	2.15475599929	0.308581306739	-0.371194212207	2.80934160308	-0.0110306456978	0.155930422116	-0.0919960507487	-0.0645709129513	0.00777187665456	0.00985297977593	0.0959233353531	0.163204548986	-0.00229164027854	0.166256709234	0.00728445104653	-0.00339001083931	0.156406329376	-0.0122355010536	0.169507246924	27.7482081744	13.6100237673	16.3734749061
37	1.99999170174	2.00000886686	-7.23271215717	1.99998807543	8.60153172651	1.53660483047	-0.736810594966	3.56938412881	-0.99808739158	-3.10065755486	0.491048708352	1.78879824296	3.57005307531	-2.94831325978	0.239224937334	0.843100491914	-0.0780276432521	0.0404298152238	0.75452243119	0.0147762373709	0.141132375584	19.243500703	39.3637934439	9.31721617256
38	1.83477324942	2.05344729041	-0.297131181719	3.34798803725	-0.584258249127	0.930543168193	0.0566193645333	-0.0775815133753	-0.1448221651	0.0773630907474	0.0249834127919	-0.0448462614978	0.163200039974	0.0688882523226	-0.0737207767692	0.161081804615	0.0331899297547	-0.0131430192208	0.160058680207	-0.0141989128821	0.180297525067	41.9781151031	18.2738997562	62.0519453042
39	0.802858749734	0.472736211311	-0.0990368098176	1.03106751028	-0.190924148232	0.216267389	0.0118558327747	-0.109111995122	-0.0518306911621	0.0367411603132	-0.0409376696373	-0.0936339247312	-0.0304480679442	0.0777395903391	0.0347622528619	0.174123109518	-0.018936437689	-0.0195101893169	0.197483220107	-0.0112313681153	0.146142880654	42.4432836542	32.2988715198	63.1905359915
40	0.922505208763	0.43331720715	-0.537953401219	0.915024257062	-0.524055666237	1.28624185493	0.0442964762618	0.0230356576084	0.0333263068207	0.0209255817566	-0.0191554408372	0.0145431969422	-0.0388281413691	0.0175671222104	-0.0237250734925	0.162282171801	-0.00787651198418	-0.0160678257288	0.16703270211	-0.0138074512728	0.164294082645	35.1422651953	39.9904502431	65.1221884003
41	2.13923728356	-0.247456415257	0.537485052334	1.63744913102	0.349208836333	2.48276413396	0.0286517030253	-0.0992654973532	-0.066565646383	0.241807853347	-0.0127057450032	0.0363465638551	0.00363321044532	-0.0900801729052	-0.00826642705904	0.197085975811	-0.0302597712204	-0.0221197973901	0.17932292664	-0.00768527052365	0.153949352057	40.3755014273	35.9400452115	89.8352867958
42	1.173845367	0.0958935261555	0.358339943042	2.5255652183	0.999725579364	2.07833991242	0.0511994360968	-0.0653564852386	-0.000851868990073	0.119066825518	0.033684185969	-0.209757777538	0.0258949881142	0.158578840203	-0.0878681615563	0.190001271989	-0.0264385206918	-0.0378796968786	0.244872018449	0.0167869737324	0.171093820341	47.7137869159	32.9633291613	87.7555950462
43	1.38500895381	-0.59969734389	0.768489878875	1.77756874866	-0.784434479319	1.29686802301	0.0563005057259	-0.0853461604306	-0.0512987253066	0.0782238749559	0.00763386375125	0.0510532397021	0.0359906697085	-0.0254798664086	-0.0817492628969	0.158651614808	-0.0305812632923	-0.0188572795418	0.169702954043	-0.00453715284084	0.119432940058	33.4370678899	27.8024290463	74.8756926917
44	2.37431351433	-2.58226404812	0.219084307145	8.55571235099	-1.12919329333	1.14186620735	0.000949339249826	-0.112007000527	-0.153169312125	0.284179916604	0.0875326344947	0.44619297006	0.0203704498719	-0.192972572941	-0.0962997962769	0.194424429701	-0.0499054622789	0.00106938535816	0.269796478474	0.00717634165218	0.184318495142	23.2915015867	24.9300085545	78.3546987512
45	1.4332217535	0.243634829369	1.58492871059	0.316521661829	0.754070667408	5.27513679746	0.0766665440644	-0.129433508481	-0.120896628955	0.110799585903	-0.0495331541945	-0.0229080675106	0.215613953051	-0.199618148997	-0.0514158919162	0.193398784388	-0.0229866619514	-0.0195508846478	0.151916961111	0.00821315382527	0.19161870224	29.7047116894	14.3542901204	65.5348196615
46	6.40942592495	-3.084454128	3.56932513926	2.38358627532	-2.38897649128	2.91828273141	0.0817710840563	-0.162102719852	0.0650877355452	0.5951996821	-0.230419119813	0.165853963489	-0.119861045132	0.199968042479	-0.0712964429368	0.880586069489	0.127733135012	0.0931219766212	0.897044270978	-0.228347778697	0.303587308989	19.84065159	49.408731256	62.2237581948
47	2.00000311555	2.00001474889	1.99996685058	2.00000990338	2.00000808029	1.99999411264	-0.470013102401	0.465176316258	-0.923534773495	0.872004943681	-0.0631850283016	4.1611112743	2.67801031385	-3.18655397174	0.506643316958	0.649121185509	-0.219223350899	0.330903305815	0.763223953551	0.260411208546	0.61315143414	8.0595557876	16.4866346388	54.2875455822

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 0 through 113 )	A	A	0 - 113	1 - 117
2	2	chain 'A' and (resid 114 through 180 )	A	A	114 - 180	118 - 187
3	3	chain 'A' and (resid 181 through 228 )	A	A	181 - 228	188 - 235
4	4	chain 'A' and (resid 229 through 273 )	A	A	229 - 273	236 - 283
5	5	chain 'A' and (resid 274 through 308 )	A	A	274 - 308	284 - 321
6	6	chain 'A' and (resid 309 through 358 )	A	A	309 - 358	322 - 371
7	7	chain 'A' and (resid 359 through 384 )	A	A	359 - 384	372 - 397
8	8	chain 'A' and (resid 385 through 411 )	A	A	385 - 411	398 - 424
9	9	chain 'B' and (resid 0 through 42 )	B	L	0 - 42	1 - 47
10	10	chain 'B' and (resid 43 through 113 )	B	L	43 - 113	48 - 118
11	11	chain 'B' and (resid 114 through 200 )	B	L	114 - 200	119 - 208
12	12	chain 'B' and (resid 201 through 287 )	B	L	201 - 287	209 - 301
13	13	chain 'B' and (resid 288 through 308 )	B	L	288 - 308	302 - 322
14	14	chain 'B' and (resid 309 through 338 )	B	L	309 - 338	323 - 352
15	15	chain 'B' and (resid 339 through 358 )	B	L	339 - 358	353 - 372
16	16	chain 'B' and (resid 359 through 384 )	B	L	359 - 384	373 - 398
17	17	chain 'B' and (resid 385 through 411 )	B	L	385 - 411	399 - 425
18	18	chain 'B' and (resid 901 through 901 )	B	N	901	3
19	19	chain 'C' and (resid 0 through 113 )	C	V	0 - 113	1 - 120
20	20	chain 'C' and (resid 114 through 200 )	C	V	114 - 200	121 - 216
21	21	chain 'C' and (resid 201 through 273 )	C	V	201 - 273	217 - 295
22	22	chain 'C' and (resid 274 through 308 )	C	V	274 - 308	296 - 330
23	23	chain 'C' and (resid 309 through 358 )	C	V	309 - 358	331 - 380
24	24	chain 'C' and (resid 359 through 384 )	C	V	359 - 384	381 - 406
25	25	chain 'C' and (resid 385 through 411 )	C	V	385 - 411	407 - 436
26	26	chain 'C' and (resid 1101 through 1101 )	C	X	1101	3
27	27	chain 'D' and (resid 0 through 161 )	D	C	0 - 161	1 - 174
28	28	chain 'D' and (resid 162 through 411 )	D	D	162 - 411	175 - 427
29	29	chain 'E' and (resid 0 through 42 )	E	E	0 - 42	1 - 43
30	30	chain 'E' and (resid 43 through 113 )	E	E	43 - 113	44 - 114
31	31	chain 'E' and (resid 114 through 183 )	E	E	114 - 183	115 - 191
32	32	chain 'E' and (resid 184 through 273 )	E	E	184 - 273	194 - 292
33	33	chain 'E' and (resid 274 through 308 )	E	E	274 - 308	293 - 327
34	34	chain 'E' and (resid 309 through 358 )	E	E	309 - 358	328 - 380
35	35	chain 'E' and (resid 359 through 384 )	E	E	359 - 384	381 - 406
36	36	chain 'E' and (resid 385 through 411 )	E	E	385 - 411	407 - 436
37	37	chain 'E' and (resid 1001 through 1001 )	E	E	1001	4
38	38	chain 'F' and (resid 0 through 42 )	F	F	0 - 42	1 - 46
39	39	chain 'F' and (resid 43 through 113 )	F	F	43 - 113	47 - 117
40	40	chain 'F' and (resid 114 through 200 )	F	F	114 - 200	118 - 210
41	41	chain 'F' and (resid 201 through 249 )	F	F	201 - 249	211 - 265
42	42	chain 'F' and (resid 250 through 308 )	F	F	250 - 308	266 - 327
43	43	chain 'F' and (resid 309 through 358 )	F	F	309 - 358	328 - 377
44	44	chain 'F' and (resid 359 through 384 )	F	F	359 - 384	378 - 403
45	45	chain 'F' and (resid 385 through 411 )	F	F	385 - 411	404 - 430
46	46	chain 'I' and (resid 3303 through 3304 )	I	I	3303 - 3304	1 - 2
47	47	chain 'I' and (resid 3305 through 3305 )	I	I	3305	1

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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

-
Protein , 1 types, 6 molecules ABCDEF

-
Non-polymers , 10 types, 2706 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

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Yorodumi