PDB-7sf2: Crystal Structure of Beta-Galactosidase from Bacteroides cellulos...

ID or keywords:

Entry

Database: PDB / ID: 7sf2

Title

Crystal Structure of Beta-Galactosidase from Bacteroides cellulosilyticus

Components

Glycosyl hydrolase family 2, sugar binding domain protein

Keywords

HYDROLASE / Glycoside hydrolase / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function

Biological species

Bacteroides cellulosilyticus DSM 14838 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.75 Å

Authors

Kim, Y. / Joachimiak, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of Beta-Galactosidase from Bacteroides cellulosilyticus
Authors: Kim, Y. / Joachimiak, G. / Endres, M. / Joachimiak, A.

History

Deposition	Oct 2, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 3, 2021	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7sf2.cif.gz	1.7 MB	Display	PDBx/mmCIF format
PDB format	pdb7sf2.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	7sf2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7sf2_validation.pdf.gz	543.9 KB	Display	wwPDB validaton report
Full document	7sf2_full_validation.pdf.gz	564.3 KB	Display
Data in XML	7sf2_validation.xml.gz	133.8 KB	Display
Data in CIF	7sf2_validation.cif.gz	187.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sf/7sf2 ftp://data.pdbj.org/pub/pdb/validation_reports/sf/7sf2	HTTPS FTP

-
Related structure data

Similar structure data	2zba-d 4bc2-d 4bc5-d 6hsz-d 4bz9-d 4bz5-d 6dep-1 6dem-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (7) #39 - Mar 2003 lac Repressor similarity (7) #234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1)

Deposited unit

A: Glycosyl hydrolase family 2, sugar binding domain protein

B: Glycosyl hydrolase family 2, sugar binding domain protein

C: Glycosyl hydrolase family 2, sugar binding domain protein

D: Glycosyl hydrolase family 2, sugar binding domain protein

E: Glycosyl hydrolase family 2, sugar binding domain protein

F: Glycosyl hydrolase family 2, sugar binding domain protein

hetero molecules

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

1

A: Glycosyl hydrolase family 2, sugar binding domain protein

B: Glycosyl hydrolase family 2, sugar binding domain protein

D: Glycosyl hydrolase family 2, sugar binding domain protein

hetero molecules

defined by author
208 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Glycosyl hydrolase family 2, sugar binding domain protein

E: Glycosyl hydrolase family 2, sugar binding domain protein

F: Glycosyl hydrolase family 2, sugar binding domain protein

hetero molecules

defined by author
207 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	335.847, 349.396, 352.108
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	22
Space group name H-M	F222
Space group name Hall	F22
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z #4: -x,-y,z #5: x,y+1/2,z+1/2 #6: x,-y+1/2,-z+1/2 #7: -x,y+1/2,-z+1/2 #8: -x,-y+1/2,z+1/2 #9: x+1/2,y,z+1/2 #10: x+1/2,-y,-z+1/2 #11: -x+1/2,y,-z+1/2 #12: -x+1/2,-y,z+1/2 #13: x+1/2,y+1/2,z #14: x+1/2,-y+1/2,-z #15: -x+1/2,y+1/2,-z #16: -x+1/2,-y+1/2,z

Components on special symmetry positions

ID	Model	Components
1	1	A-927- HOH
2	1	B-856- HOH
3	1	D-921- HOH

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein	Glycosyl hydrolase family 2, sugar binding domain protein Mass: 68149.805 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides cellulosilyticus DSM 14838 (bacteria) Gene: BACCELL_01794 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pGrow7-K / References: UniProt: E2NBY7

#1: Protein

Glycosyl hydrolase family 2, sugar binding domain protein

Mass: 68149.805 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacteroides cellulosilyticus DSM 14838 (bacteria)
Gene: BACCELL_01794 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pGrow7-K / References: UniProt: E2NBY7

-
Non-polymers , 7 types, 1678 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 58 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#6: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS
#7: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO₄
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1584 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 6.32 Å³/Da / Density % sol: 80.52 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-HCl, pH 8.5, 2.4 M ammonium phosphate dibasic

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 10, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.75→48.11 Å / Num. obs: 255513 / % possible obs: 96.5 % / Redundancy: 4.8 % / B_iso Wilson estimate: 28.06 Å² / CC_1/2: 0.987 / R_merge(I) obs: 0.149 / Net I/σ(I): 8.3
Reflection shell	Resolution: 2.75→2.8 Å / R_merge(I) obs: 0.658 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 12805 / CC_1/2: 0.798

-
Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.75→48.1 Å / SU ML: 0.3043 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.8519
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2094	12548	5.22 %
R_work	0.1817	227714	-
obs	0.1831	240262	90.77 %

Solvent computation

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

Displacement parameters

B_iso mean: 31.48 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→48.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28503	0	349	1584	30436

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0021	30225
X-RAY DIFFRACTION	f_angle_d	0.4937	41052
X-RAY DIFFRACTION	f_chiral_restr	0.0434	4227
X-RAY DIFFRACTION	f_plane_restr	0.0046	5323
X-RAY DIFFRACTION	f_dihedral_angle_d	13.83	11203

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 (%)
2.75-2.78	0.3398	361	0.2945	7410	X-RAY DIFFRACTION	88.76
2.78-2.81	0.3207	408	0.2737	7584	X-RAY DIFFRACTION	90.97
2.81-2.85	0.324	367	0.2638	7633	X-RAY DIFFRACTION	91.13
2.85-2.88	0.3082	384	0.259	7609	X-RAY DIFFRACTION	90.91
2.88-2.92	0.2932	454	0.2698	7472	X-RAY DIFFRACTION	90.43
2.92-2.96	0.2977	507	0.2571	7520	X-RAY DIFFRACTION	91.55
2.96-3	0.2851	513	0.25	7483	X-RAY DIFFRACTION	91.25
3-3.05	0.304	462	0.2465	7566	X-RAY DIFFRACTION	91.29
3.05-3.1	0.2862	444	0.239	7636	X-RAY DIFFRACTION	91.69
3.1-3.15	0.2844	416	0.2391	7500	X-RAY DIFFRACTION	90.6
3.15-3.2	0.2697	442	0.2343	7630	X-RAY DIFFRACTION	91.38
3.2-3.26	0.2679	427	0.2249	7546	X-RAY DIFFRACTION	90.67
3.26-3.32	0.2464	359	0.2127	7480	X-RAY DIFFRACTION	89.48
3.32-3.39	0.2222	339	0.2046	7521	X-RAY DIFFRACTION	89.37
3.39-3.46	0.2363	417	0.1946	7490	X-RAY DIFFRACTION	89.77
3.46-3.55	0.2063	401	0.1882	7474	X-RAY DIFFRACTION	89.54
3.55-3.63	0.1992	425	0.1788	7504	X-RAY DIFFRACTION	90
3.63-3.73	0.2035	402	0.1758	7454	X-RAY DIFFRACTION	89.18
3.73-3.84	0.1803	422	0.1632	7501	X-RAY DIFFRACTION	90.05
3.84-3.97	0.183	434	0.1527	7539	X-RAY DIFFRACTION	90.56
3.97-4.11	0.1691	445	0.148	7525	X-RAY DIFFRACTION	90.11
4.11-4.27	0.1632	464	0.1363	7545	X-RAY DIFFRACTION	90.77
4.27-4.47	0.1564	430	0.1318	7479	X-RAY DIFFRACTION	89.85
4.47-4.7	0.1392	436	0.125	7702	X-RAY DIFFRACTION	92.06
4.7-5	0.1373	376	0.1199	7795	X-RAY DIFFRACTION	92.25
5-5.38	0.1443	402	0.1282	7817	X-RAY DIFFRACTION	92.62
5.38-5.92	0.1454	423	0.1322	7851	X-RAY DIFFRACTION	93.03
5.92-6.78	0.172	430	0.1514	7705	X-RAY DIFFRACTION	91.46
6.78-8.53	0.1654	373	0.1459	7928	X-RAY DIFFRACTION	92.72
8.53-48.1	0.1753	385	0.1696	7815	X-RAY DIFFRACTION	89.62

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	1.84069330875	0.226693399922	0.461716855692	1.13099029257	-0.126543963866	1.57219512666	-0.0198060625416	0.00502362169435	0.395137860256	-0.0563989241705	0.0120847339495	0.184778489968	-0.212140982771	-0.0475209090424	0.00083669806131	0.168393060354	0.00452579079837	-0.0343892724207	0.118698803416	-0.0317410472739	0.251211620035	38.473	88.75	69.652
2	2.98616746465	0.827069126159	0.044825423131	1.72095513902	0.0704069477962	2.23920400388	-0.0952873225098	0.36429693338	0.495035507969	-0.418713639768	0.121012639818	0.16698225994	-0.253045261305	-0.247963048875	0.11748890146	0.192783787442	0.0272320835889	-0.0627000253214	0.131130347106	0.00891457942896	0.228000759352	35.717	83.463	59.945
3	0.532994654155	0.194787586778	0.068965500119	0.539301349363	0.145918212857	0.563263995046	0.00220120819368	0.00791870290721	0.0457525281661	0.0150281720053	9.95248599903E-5	0.0782797613631	0.0877333903777	-0.0826577541937	-0.011208873867	0.161487613837	-0.0460915773565	-0.0251194413381	0.185554364917	-0.0356613209273	0.173710360293	33.747	63.631	74.622
4	2.26293900432	0.160212067587	-0.294012949962	4.41042947846	-0.628531646628	1.14008593869	0.00875237960788	0.00676583821156	0.229680073901	-0.0507537275594	-0.0258287696673	0.662437895298	-0.0390844923551	-0.380431896102	-0.0234822919667	0.150709924186	-0.0324623202922	-0.015522407091	0.32810662867	-0.101534727952	0.277184895528	9.781	68.094	73.792
5	1.26231742836	-0.142810696023	0.235790943024	1.10614094399	0.31072556508	1.55972329224	-0.00679038783467	0.132302767453	-0.0306290240013	-0.148344009281	0.0238941158902	-0.146548573155	-0.0857867749117	0.447351523985	-0.00957008534053	0.119333826768	-0.0823626065305	0.0175139603633	0.327981131488	-0.00582911960472	0.179481527624	85.286	69.235	43.004
6	2.69016082756	0.513170564431	1.44664027317	3.00505664121	0.410165291516	2.16379005252	0.300675061494	0.0780815105367	-0.437565178102	-0.260824257561	-0.0409441636926	-0.277416146646	0.398313756035	0.604223645541	-0.430005769966	0.0942660390393	-0.0673663195107	0.0405819502188	0.351691789135	-0.0265907979046	0.151484688358	79.961	59.357	39.293
7	0.597260799826	-0.101168414386	-0.245761153294	0.391870241222	0.411374102052	1.36680342276	-0.118096453776	-0.0240442706289	0.0973246117829	-0.0576850596971	0.0451504165214	0.0900959790993	-0.150681716487	0.0611649740497	0.0758309845553	0.181003409163	-0.0890545299969	-0.0236416930036	0.156793594961	0.007479655774	0.180236707615	62.783	83.523	48.803
8	0.723896918421	0.114429645935	0.358910020004	0.507159519418	0.12407690024	0.464836770698	0.00228583549876	0.0847503133064	0.0164596203775	-0.113235358024	0.000159480352331	0.0606757881117	-0.0171434940599	0.0516565979114	-0.0134499173942	0.213952994446	-0.0795247453385	-0.0342769766344	0.213722760557	0.00610780811296	0.154436709166	59.956	71.26	35.477
9	2.59114643828	0.175076773791	-0.156810466509	0.848944138697	0.112246259229	1.84391495519	0.00847028215123	0.543850122187	-0.00388051257653	-0.340345881962	-0.00109225744197	-0.016546740309	-0.128453869655	0.198154340783	-0.00159896597853	0.352976966707	-0.120611456782	-0.0421189101004	0.343366310994	0.0122383028762	0.144213989206	62.308	72.063	14.995
10	4.14372702065	2.96477321555	-2.28335482564	7.3446044389	3.96797807623	7.26549918461	-1.02916145936	0.771677171872	0.478902906534	-0.947142147587	1.46633500861	0.849410988996	0.762729761653	-0.859291298366	-0.435131841242	0.897311799776	-0.183944671054	-0.10576906808	0.993050171796	0.17054731079	1.27065507548	42.342	88.17	24.772
11	1.05245612757	0.151627776574	-0.288153126335	2.38686431728	0.244148111229	1.39217811915	-0.00177262164885	0.0874795035891	0.0222190862921	-0.0403938893535	-0.00747258876382	0.242629482827	0.0462395045492	-0.295018916996	0.0157088615008	0.148096984403	-0.0610322336262	-0.0841253178321	0.318804260272	0.0146990126568	0.194250422392	-5.494	46.549	22.586
12	2.21089293879	1.64412382501	0.968264173375	4.69032929269	0.897223263719	1.94292296858	0.114127389163	-0.154301674306	0.162384559391	0.585362024029	-0.130146912302	0.372102304162	-0.0215329565414	-0.23591573565	0.0976454061209	0.15204486335	-0.0306106100396	-0.0791944026924	0.360917091028	0.0220934507093	0.132501879463	0.21	50.939	32.205
13	0.520864182152	-0.0586326031474	-0.390641457015	0.679239085895	0.383457814842	0.529832516242	-0.118779511823	0.114544846595	-0.111868870628	0.050574364752	0.110602208036	-0.0114967044157	0.0758675469214	0.0520650081855	0.00218406879261	0.233839686703	-0.0603272282377	-0.103429343019	0.303118002766	-0.018823302021	0.194701428861	13.485	41.342	11.399
14	0.232589296433	0.384966387417	-0.283831302154	4.69762906572	0.388591220274	0.474504788456	-0.218687188001	0.25553612458	-0.0307730771775	-0.35277317574	0.0605302466568	-0.22310214826	0.0650487090972	0.064790062854	0.115628865072	0.267646754483	-0.0750392603903	-0.116007609287	0.375571164957	-0.00825713834208	0.160120781917	21.832	45.446	-1.469
15	0.898850956096	0.555309686179	0.0940501581005	0.748949611687	0.13683760102	0.47232326574	0.0028686761796	0.10931903181	0.0413791632511	-0.00146293835944	-0.00199846650987	0.03208458721	-0.0839262925176	0.00141507233069	-0.002836080969	0.238103126411	-0.0582821669869	-0.105079380051	0.256763128001	0.0194710032128	0.19023718908	19.199	58.557	18.97
16	4.38765991551	-0.0913455296643	-1.10478649101	1.81607661288	-0.272261110985	1.88488417426	0.0775773549864	0.0891993391447	0.723613307046	-0.0675805605823	0.0806627853186	0.266764061413	-0.4796838473	-0.114477809622	-0.144709936434	0.415383549625	-0.0158626483712	-0.166292505695	0.191999197471	0.0704905486249	0.301090850542	11.005	77.653	16.901
17	1.62996207722	0.418600588033	-0.404908639655	2.07254470764	0.0767081561151	1.12317284468	-0.039893749532	-0.101093699768	-0.111397383503	0.369985895663	0.031981788917	-0.0555047715707	0.209334050777	-0.0272447447455	0.007089495223	0.234387412765	-0.016682900704	-0.068580075228	0.187712697672	0.0286720830111	0.12187948439	65.472	42.168	89.25
18	2.76154008084	0.150591625646	0.0116329598108	3.48093471129	-0.00794339017674	1.17513512258	0.0389200685359	-0.299629300568	-0.157545150124	0.395633560834	-0.200497523491	0.284857253905	0.290366715264	-0.317967457932	0.190984715655	0.173992776446	-0.0844850787656	0.00918493088962	0.205708038024	0.0672040025425	0.117352600102	56.187	39.32	83.985
19	0.585262071252	0.451805587762	-0.0840615314362	0.681965568253	-0.0251772639648	1.07072964348	0.00644501171687	0.0944937134332	-0.0549222386763	0.0536155022797	0.00383008965097	-0.0891788640837	-0.0789780971428	0.12742303693	-0.0248979457951	0.131932359461	0.0112269073855	-0.0642748473699	0.181619001246	0.0053142646779	0.204427270639	75.595	49.18	70.204
20	0.678090667743	0.12655608505	0.0670196139859	0.477481969749	0.195814439575	0.672763871871	-0.015694035474	0.0476129346746	-0.0848497864543	0.0554740896623	0.011377518931	-0.0354961803106	0.148801306008	0.0594068914803	0.00592774545788	0.183122551242	-0.00503563694137	-0.0538210692858	0.162938210664	-0.0232791566767	0.200062715356	69.122	34.594	62.542
21	0.980156493535	-0.559743668127	-0.167404520568	1.95322325687	-0.25523789872	2.98689738959	-0.0796671470474	-0.0385339426372	-0.338766024657	0.190059092736	0.0601827696522	-0.0157322652034	0.85328335555	-0.0267510328614	0.0943241917938	0.426677100704	0.0139438404079	-0.0941267159163	0.161501878689	0.00144623616179	0.37877257471	69.138	13.069	68.763
22	2.00032004297	1.99699154061	2.00459878622	1.99785063331	1.99839991053	2.01044896975	0.273477621992	0.354960196377	-0.0752775374126	0.0626197483927	-0.220355431457	-0.0106878349589	-0.607741232313	-0.43141957611	-0.0687009128239	0.76010621895	0.298301002315	-0.171730189542	0.891828522323	0.00267056685705	1.06192127337	84.002	23.86	45.572
23	0.941356164046	-0.0424234393564	0.438349020589	0.487225291009	0.267818157621	1.5016826159	0.00810847637694	0.00173844190691	-0.135070222468	-0.0150846662467	0.0454860185298	-0.0720555593947	0.265010926855	0.0217771432688	-0.0628203881496	0.265402516934	-0.116681406857	-0.0153785386467	0.170227955778	-0.0180563510993	0.271003248834	17.803	-1.308	45.492
24	1.16694378371	0.254803438122	-0.0188145543115	2.14559386422	1.11934523	2.9731638656	-0.121823396147	-0.0537433032392	-0.195466051815	-0.0102220784479	0.0728444790609	-0.227674734396	0.193533946332	0.300499877171	-0.260667461137	0.231773433722	-0.124685781857	-0.0495162587089	0.121639958682	0.0280765382396	0.338453316567	26.818	4.086	49.204
25	0.57639612033	-0.21839073405	0.230934532703	0.828577267411	-0.0293858215984	0.784296267679	0.0363319884989	0.0349054625171	0.134248871462	-0.142308931173	-0.0904345026845	-0.0720094980574	0.00576168858568	-0.0244617687762	0.0605041770152	0.241922966931	-0.155255680988	-0.0225607227346	0.210736040609	0.0185397263133	0.212182180285	6.865	18.057	40.897
26	0.135182923739	0.0758150400405	-0.613060317669	0.900999317945	-0.636951635209	3.13892239697	-0.0271043489465	0.138639576702	0.252711953564	0.220501836991	0.20891787529	0.314787197609	-0.338622549423	0.0201949308051	-0.162014880754	0.0721192250357	-0.246502614868	-0.00947519517653	0.341426210804	0.0417562075505	0.333136410501	-5.912	26.353	45.241
27	0.510844453135	0.104545920245	0.0982540136196	0.621234412444	0.478186232373	0.64258587416	-0.00220731814726	-0.0692684612022	0.048411932511	0.0497781916283	0.0456586454308	0.0232034100754	-0.0155709822424	-0.0523919406405	-0.022378328751	0.231998649697	-0.172199859312	-0.0169130931284	0.233744813058	-0.0243450731497	0.23273706505	14.596	23.158	58.285
28	2.38270737849	-3.26727343622	-0.683890346977	7.15423402642	1.84562244548	2.54466474547	-0.0246799983238	-0.408451918328	-0.0028438445308	0.646257672053	0.10428127172	-0.357955208372	0.361124729092	-0.0207145585553	-0.0777744192664	0.377161219421	-0.179455664594	-0.0354483352563	0.359582695317	0.0194003268035	0.23233290916	15.699	11.819	80.282
29	1.64054833533	-1.30965686332	0.0761316077147	4.91645418883	-0.558652266266	0.811654576865	0.165730000208	-0.465407150975	-0.121797495253	0.222677763953	-0.123314983598	0.156536023695	0.0194232731455	-0.247607377844	-0.0267862825744	0.30486196239	-0.232213981862	-0.0151109032511	0.374952786037	-0.0139771122243	0.18045039181	9.26	16.74	74.104
30	4.54814950583	1.49929433944	2.14582187028	7.74009318785	-5.61387113482	6.52679360312	2.91537640847	0.71023482397	-0.362728900255	7.36134959635	-2.20700719111	-0.699201057241	-5.27278137329	0.406334633045	-0.704832701012	1.037905195	-0.222796363229	0.256132736334	0.872917561305	-0.100287881624	0.954257172012	-4.17	37.433	69.595
31	1.32564972736	0.22249150495	0.364575775477	0.711288896606	0.280536671815	1.76645831267	-0.0894743335401	0.640366183662	-0.397019667031	-0.288281741378	0.0760238193139	-0.234722276293	0.0988239156077	0.265705608514	-0.0206789817677	0.434755292631	-0.0433243969577	0.0369614697027	0.491620547184	-0.15825153551	0.251190514743	48.265	13.703	-2.488
32	2.02356810268	0.338513072099	0.539754743603	1.61586954645	0.0931198142681	1.42997582372	-0.016158417706	0.416052343463	0.0421379973086	-0.175467224744	-0.0498928757675	0.0165561917727	-0.0847172408366	0.0561124952678	0.0579090999461	0.27309548768	-0.0752624708785	-0.019714613267	0.414801523768	-0.054858349011	0.137043693488	38.446	26.409	-1.126
33	1.66503391926	-1.05497012944	0.633704689571	1.9406890133	-0.134986994339	2.21214377226	-0.304524194039	0.572452670396	0.417780844453	-0.297225336504	0.0445707837068	-0.114491072698	-0.244023961605	0.261833611224	0.240024735423	0.321412588197	-0.133511709286	0.0686753367443	0.361956452041	-0.0532885014787	0.104013410547	45.22	31.343	3.928
34	1.02965940515	0.541500947002	-0.295672132855	0.939372652588	-0.111244710221	0.883329054347	-0.011710736001	0.257948982289	-0.127728859235	0.153962410457	0.0816468586168	0.0154048661698	0.177937830739	-0.0941316091092	-0.0609120871386	0.278175465522	-0.0611847428058	0.00885636924917	0.242706414588	-0.0973649680748	0.21935209028	36.631	11.242	17.347
35	5.4098463019	-0.480775625435	0.188382259016	1.15626880513	-0.0510098633416	0.510331070575	-0.0508703358984	-0.158677610962	-0.197230941494	0.0947738049809	0.138479927788	-0.0327324853679	0.31000745698	0.0291389254318	-0.0916042744948	0.367509873125	-0.0508849669756	0.0158720438245	0.16765728889	-0.0897708809271	0.304922433822	40.749	-1.625	25.536
36	7.23548333733	1.09227743693	3.55340001142	1.42761761418	0.859494777657	2.68769290483	-0.019576654643	0.210055908355	-0.390007350267	0.0428137053295	0.116716120379	-0.127695522301	0.0994191124193	0.0629985007108	-0.141237117305	0.321559683929	-0.016214421953	0.0250525888332	0.121559517026	-0.0487960694723	0.202363297001	43.592	5.047	25.578
37	0.72889534434	-0.0895061893643	-0.0158444633802	0.782015036124	0.00356789343303	0.793937705597	-0.0667670054957	0.149848786019	-0.0680596976673	-0.0440306098874	0.0240651015086	-0.104357342926	0.0390346673118	0.0916098405107	0.0467768261555	0.199204833369	-0.0454346723785	-0.0205172121126	0.238544709492	-0.0702078602386	0.2211695708	56.184	21.461	22.351
38	2.33280128272	-0.229954413288	-0.308584690583	2.04400485862	-1.62102627085	5.19637463774	-0.0428140829135	0.36242871609	-0.0975904583453	-0.18190575663	0.00541434391202	-0.451613481815	0.0805899117412	0.598349223787	0.0883318809424	0.211172865195	-0.0111191310712	0.0596596675088	0.402302769987	-0.15528037596	0.369582013855	72.989	16.474	14.349
39	3.2053789867	-4.97984215479	-4.79725546087	9.77892791651	8.21521297354	7.46391612953	-0.00400657162952	-6.75558410407	1.64205179185	-0.899448616458	2.92738005142	-0.440727361125	-0.740458891572	6.12025564007	-2.95599765338	1.0418752016	0.461321307747	-0.000764102945122	0.854998906864	-0.0796523080741	1.033186709	65.037	-0.229	37.126

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 20:159 )	A	20 - 159
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 160:193 )	A	160 - 193
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 194:516 )	A	194 - 516
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 517:605 )	A	517 - 605
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 20:159 )	B	20 - 159
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 160:193 )	B	160 - 193
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 194:284 )	B	194 - 284
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 285:491 )	B	285 - 491
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 492:604 )	B	492 - 604
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 605:605 )	B	605
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 20:159 )	C	20 - 159
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 160:193 )	C	160 - 193
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 194:250 )	C	194 - 250
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 251:284 )	C	251 - 284
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 285:516 )	C	285 - 516
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 517:604 )	C	517 - 604
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 20:159 )	D	20 - 159
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 160:193 )	D	160 - 193
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 194:250 )	D	194 - 250
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 251:516 )	D	251 - 516
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 517:604 )	D	517 - 604
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 605:605 )	D	605
23	X-RAY DIFFRACTION	23	( CHAIN E AND RESID 20:159 )	E	20 - 159
24	X-RAY DIFFRACTION	24	( CHAIN E AND RESID 160:193 )	E	160 - 193
25	X-RAY DIFFRACTION	25	( CHAIN E AND RESID 194:250 )	E	194 - 250
26	X-RAY DIFFRACTION	26	( CHAIN E AND RESID 251:284 )	E	251 - 284
27	X-RAY DIFFRACTION	27	( CHAIN E AND RESID 285:516 )	E	285 - 516
28	X-RAY DIFFRACTION	28	( CHAIN E AND RESID 517:555 )	E	517 - 555
29	X-RAY DIFFRACTION	29	( CHAIN E AND RESID 556:604 )	E	556 - 604
30	X-RAY DIFFRACTION	30	( CHAIN E AND RESID 605:605 )	E	605
31	X-RAY DIFFRACTION	31	( CHAIN F AND RESID 20:60 )	F	20 - 60
32	X-RAY DIFFRACTION	32	( CHAIN F AND RESID 61:159 )	F	61 - 159
33	X-RAY DIFFRACTION	33	( CHAIN F AND RESID 160:193 )	F	160 - 193
34	X-RAY DIFFRACTION	34	( CHAIN F AND RESID 194:250 )	F	194 - 250
35	X-RAY DIFFRACTION	35	( CHAIN F AND RESID 251:284 )	F	251 - 284
36	X-RAY DIFFRACTION	36	( CHAIN F AND RESID 285:324 )	F	285 - 324
37	X-RAY DIFFRACTION	37	( CHAIN F AND RESID 325:516 )	F	325 - 516
38	X-RAY DIFFRACTION	38	( CHAIN F AND RESID 517:604 )	F	517 - 604
39	X-RAY DIFFRACTION	39	( CHAIN F AND RESID 605:605 )	F	605

-
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://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

-
Protein , 1 types, 6 molecules ABCDEF

-
Non-polymers , 7 types, 1678 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

-
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 , 7 types, 1678 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

-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 , 7 types, 1678 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

-
Yorodumi