PDB-7k1r: X-ray Structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 ...

ID or keywords:

Entry

Database: PDB / ID: 7k1r

Title

X-ray Structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 F507A mutant

Components

Beta xylosidase GH43

Keywords

HYDROLASE / Glycoside Hydrolase / GH43 / Beta-xylosidase / Enterobacter

Function / homology

Function and homology information

xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function

Biological species

Enterobacter sp. enrichment culture clone nf1B6 (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Briganti, L. / Capetti, C.C.M. / Polikarpov, I.

Funding support

Brazil, 3items

Organization	Grant number	Country
Sao Paulo Research Foundation (FAPESP)	2015/13684-0	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	423693/2016-6	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	303988/2016-9	Brazil

Citation

Journal: To Be Published
Title: X-ray Structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 F507A mutant
Authors: Briganti, L. / Capetti, C.C.M. / Polikarpov, I.

History

Deposition	Sep 8, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 10, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7k1r.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb7k1r.ent.gz	721.9 KB	Display	PDB format
PDBx/mmJSON format	7k1r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k1/7k1r ftp://data.pdbj.org/pub/pdb/validation_reports/k1/7k1r	HTTPS FTP

-
Related structure data

Related structure data	2exhS S: Starting model for refinement
Similar structure data	1yif-d 2exk-d 2exi-d 1y7b-d 1yi7-d 5zqx-d 2exj-d 2exh-d 3c2u-d 1m6x-d 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

Deposited unit

A: Beta xylosidase GH43

B: Beta xylosidase GH43

C: Beta xylosidase GH43

D: Beta xylosidase GH43

hetero molecules

244 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta xylosidase GH43

D: Beta xylosidase GH43

hetero molecules

B: Beta xylosidase GH43

hetero molecules

C: Beta xylosidase GH43

hetero molecules

defined by author&software
244 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.123, 153.100, 182.401
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

#1: Protein	Beta xylosidase GH43 Mass: 60924.859 Da / Num. of mol.: 4 / Mutation: F507A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter sp. enrichment culture clone nf1B6 (environmental samples) Production host: Escherichia coli (E. coli) / References: UniProt: V5J3M5, xylan 1,4-beta-xylosidase
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1395 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 4M Sodium Formate

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

LNLS

/ Beamline: W01B-MX2 / Wavelength: 1.45 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 27, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.45 Å / Relative weight: 1

Reflection

Resolution: 2.4→49.15 Å / Num. obs: 95985 / % possible obs: 99.9 % / Redundancy: 13 % / B_iso Wilson estimate: 37.98 Å² / CC_1/2: 0.993 / R_pim(I) all: 0.08 / R_rim(I) all: 0.291 / Net I/σ(I): 8.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Num. unique obs	CC_1/2	R_pim(I) all	% possible all	R_merge(I) obs	R_rim(I) all
2.4-2.44	11.8	4619	0.39	0.777	98.2
2.4-49.15	10.6	676	0.998	0.025	98.3	0.085	0.089

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
Aimless	0.7.3	data scaling
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
PHASER	1.14-3260	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2EXH

2exh

Resolution: 2.4→22.72 Å / SU ML: 0.3032 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4772
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2275	4608	4.81 %
R_work	0.19	91143	-
obs	0.1918	95751	99.89 %

Solvent computation

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

Displacement parameters

B_iso mean: 41.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→22.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17109	0	16	1395	18520

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0021	17720
X-RAY DIFFRACTION	f_angle_d	0.5707	24208
X-RAY DIFFRACTION	f_chiral_restr	0.0437	2460
X-RAY DIFFRACTION	f_plane_restr	0.0039	3151
X-RAY DIFFRACTION	f_dihedral_angle_d	5.6938	2374

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 (%)
2.4-2.43	0.3341	147	0.3139	2927	X-RAY DIFFRACTION	97.37
2.43-2.46	0.3168	140	0.2871	3010	X-RAY DIFFRACTION	100
2.46-2.49	0.3173	150	0.2852	3030	X-RAY DIFFRACTION	99.97
2.49-2.52	0.3479	153	0.2842	2972	X-RAY DIFFRACTION	100
2.52-2.55	0.3069	164	0.2882	3010	X-RAY DIFFRACTION	100
2.55-2.59	0.2739	156	0.2824	3017	X-RAY DIFFRACTION	100
2.59-2.62	0.3199	119	0.274	3015	X-RAY DIFFRACTION	100
2.62-2.66	0.303	130	0.2552	3042	X-RAY DIFFRACTION	100
2.66-2.7	0.3052	170	0.2614	3002	X-RAY DIFFRACTION	99.97
2.7-2.75	0.3076	169	0.2554	2959	X-RAY DIFFRACTION	100
2.75-2.79	0.2739	171	0.2517	3032	X-RAY DIFFRACTION	100
2.79-2.84	0.2884	155	0.2525	3013	X-RAY DIFFRACTION	100
2.84-2.9	0.2962	162	0.2447	3032	X-RAY DIFFRACTION	100
2.9-2.96	0.2839	150	0.2419	2987	X-RAY DIFFRACTION	100
2.96-3.02	0.2465	139	0.2346	3048	X-RAY DIFFRACTION	100
3.02-3.09	0.3016	157	0.2292	3034	X-RAY DIFFRACTION	100
3.09-3.17	0.2696	157	0.2219	2986	X-RAY DIFFRACTION	100
3.17-3.26	0.2442	157	0.2097	3050	X-RAY DIFFRACTION	100
3.26-3.35	0.221	149	0.1948	3037	X-RAY DIFFRACTION	100
3.35-3.46	0.2101	158	0.1827	3044	X-RAY DIFFRACTION	100
3.46-3.58	0.2031	155	0.1664	3015	X-RAY DIFFRACTION	100
3.58-3.72	0.193	156	0.1532	3043	X-RAY DIFFRACTION	99.97
3.72-3.89	0.2055	165	0.1551	3045	X-RAY DIFFRACTION	100
3.89-4.1	0.1928	153	0.1432	3056	X-RAY DIFFRACTION	99.94
4.1-4.35	0.1612	153	0.1352	3071	X-RAY DIFFRACTION	100
4.35-4.69	0.1779	145	0.13	3077	X-RAY DIFFRACTION	99.91
4.69-5.15	0.142	148	0.1255	3101	X-RAY DIFFRACTION	99.97
5.15-5.89	0.2016	146	0.1559	3114	X-RAY DIFFRACTION	99.97
5.89-7.37	0.1892	147	0.1667	3145	X-RAY DIFFRACTION	100
7.38-22.72	0.2116	187	0.1802	3229	X-RAY DIFFRACTION	99.56

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	1.24349377928	0.300838997949	-0.124912732179	1.56659199028	-0.317519650443	0.665873080657	-0.0970967435993	0.152844124188	0.091740286158	-0.152950501221	0.0442899428911	-0.0183827197237	0.101066589955	-0.131053561923	0.0614285960243	0.269327614743	0.00186377873362	-0.00361660797351	0.332227863464	-0.00404354233326	0.274620216559	16.0433243403	63.4417484253	71.4480448016
2	0.526601472899	0.595818315428	-0.0577046686708	1.9024725104	0.294345478612	3.48772791779	-0.111330163314	-0.131342908909	0.165380515747	-0.000866870250166	0.0734994037145	0.252412530495	-0.1251822909	-0.594302631714	0.061764753314	0.283596458736	0.0675080797452	-0.0149796517688	0.397684406792	0.031854981161	0.400785651284	6.6134296413	76.6924406153	79.7550669693
3	1.90734253122	-0.14731809899	0.532062359144	1.68142342774	-0.167800109854	1.99722245997	-0.0684170991801	-0.220942522222	0.0166215960602	0.140693636365	0.0342086351715	0.203251217553	0.0122602616707	-0.333337301182	0.012849284217	0.235889731548	0.0047996900332	0.0371265565081	0.348508596667	-0.00284734762102	0.258057299165	9.25737984382	59.9958037676	89.3823049229
4	2.33841191403	0.629328656918	-0.720857881321	0.865606331577	-0.441791950917	1.24916894534	-0.136050597689	0.369690645734	-0.24374388759	-0.173640988006	0.0690190750574	-0.131709062897	0.259287329865	-0.0554626407991	0.0710203860505	0.289031377463	0.00277206517465	0.000757816090434	0.293045879748	-0.0485531431609	0.241977228741	30.1698822795	53.0168554786	70.0151375437
5	0.113529893108	0.352526291577	0.220629080806	2.27883515244	-0.385203157272	2.84725659181	-0.207962705965	-0.0123302219942	-0.0243337023703	0.0939377310048	-0.0855915557087	-0.333836586071	0.145468681842	0.498624495051	0.279074637552	0.235076405694	0.0558340403708	0.0047307827172	0.346510743675	0.0159106469016	0.353775612814	48.9256315884	59.6119744284	73.9346258567
6	1.87077875059	-0.21232966398	-0.246869167754	1.31956264989	-0.208011356173	1.80980760067	-0.0475610120566	0.113194850469	-0.282499325444	-0.0454480704656	-0.095303363114	-0.214827537461	0.261903554976	0.169962050315	0.124496903665	0.24025486042	0.0349049956501	-0.0111492625401	0.308835711063	0.0112211893863	0.333770097302	43.5070708864	53.5676008953	77.0224052516
7	1.28620898048	0.32106307929	-0.715282721946	1.02592741478	-0.164171651092	0.856518002375	-0.0074153526689	-0.199041557607	-0.15783315241	0.156868676991	-0.106324550136	-0.133697361688	0.215140744266	0.412976911508	0.0994775284869	0.380893995519	0.0678946193389	0.00947523856699	0.452812090071	0.0729262435015	0.287782359324	20.6610679476	83.8404208457	41.1551649299
8	2.70715202642	0.0295009013336	0.7729993775	1.26517858642	-0.198942008602	3.32424837906	-0.109694185432	-0.191308533556	-0.0162216444948	0.256379159911	0.0778386264033	-0.0260932927537	-0.120182007923	0.245879455781	0.0381364783992	0.329691559542	0.0594490614034	0.006744028698	0.287126527584	-0.00808982526428	0.26391986413	9.48895973378	94.5433628941	37.7722538576
9	1.04220135822	-0.129797723101	0.133676200363	0.791895718634	-0.166300017259	0.995686585373	-0.0329038195654	-0.0736462529255	0.129876087932	0.118986781897	-0.0399870794639	-0.0729396818801	-0.158281386414	0.194336555141	0.0562805915985	0.326500961867	-0.00108623562289	-0.0205747135816	0.364199296978	0.0343274367517	0.283146371063	21.8924674925	96.5275050222	28.17838377
10	1.89482702269	0.163429026857	0.0640004007551	3.45256191268	1.77328576745	1.36867221275	-0.0283836006916	-0.195413098585	-0.101349742581	-0.18913670449	0.0832018718976	-0.359990181091	0.0764400704704	0.749293924683	0.0196762419774	0.290086899229	-0.000390515208219	0.0151077797874	0.722320112549	0.0535439073333	0.328825979214	35.4144819632	93.3564458883	33.1564364786
11	2.07683287994	0.413308254236	-0.12059843876	1.506103724	-0.338725769901	1.21232171889	-0.0275378060207	-0.0623982264036	-0.214660561586	0.18803112444	-0.0687800514647	-0.0332871984028	0.322554018288	0.0937650540312	0.0880965461784	0.513488250494	0.0921964740393	0.0755038235445	0.286777860566	0.0713903069424	0.299172286409	10.6211228419	62.1417989281	36.2276209836
12	1.42253707951	-0.212554264186	-0.356337675016	1.46480577511	0.0734367575731	2.109982928	-0.0494554962857	-0.0524154967788	-0.279108877628	0.116519288029	-0.0415711047788	-0.128205806931	0.40537752929	0.251164301306	0.0685258771204	0.461503321042	0.113838758997	0.0532392554376	0.305856844444	0.0430090489887	0.325108160992	14.9116571607	59.8132296096	28.8013772474
13	1.20144487144	-0.345170604112	0.41426043445	0.866009168088	0.238850072137	1.12990160312	-0.111489706146	-0.15701242299	-0.0707151526964	0.265603602588	0.0184660630602	0.256453259617	0.227519495224	-0.382598026344	0.0615440125359	0.458785216299	-0.074009647752	0.12941452951	0.331911216702	0.00674482172095	0.391194440966	63.8812908395	69.6969980415	31.7370422341
14	1.86070134183	-0.224497782741	0.544778935174	0.979319247368	-0.301628821208	1.19284312724	0.0308232212121	-0.0578354267795	-0.338456348436	0.184768480364	-0.018605463968	0.245340980445	0.610382430564	-0.236474427971	-0.0575862600471	0.611238065198	-0.144842852823	0.16276344127	0.347815953197	-0.0533851103057	0.482915556239	65.7919490784	54.8628673387	22.6774679148
15	0.841595113423	0.1965126648	-0.0516775100643	1.33306798334	-0.00823499291078	0.916007217465	-0.0451786401109	0.0565093622016	0.0270423559439	0.00696397909141	-0.00840300555766	0.171256644608	0.0279749159013	-0.28598283174	0.0513682159867	0.259266661405	0.0141531748427	0.0448332377461	0.362100456518	0.0215203604499	0.269805812492	67.2925291987	88.5143111808	21.2344268213
16	0.876408754232	-0.0156105106722	-0.293980899123	2.07195441817	-0.0586530422193	1.31862061203	0.0956956215903	0.165408835595	0.467051505923	-0.0618706289335	0.0623727258392	-0.0860039444766	-0.570235112593	0.0678406144398	0.0878726420514	0.533348445075	-0.190621594309	-0.0732389912343	0.510586545142	0.146062119928	0.51080665933	55.2825083662	100.642377413	66.9094257322
17	0.856646192289	-0.298063529917	-0.195300121509	2.12208838567	-0.119995611309	1.82923284283	-0.0194810738131	0.28677248261	0.298763100366	0.0408633878576	-0.076221052017	0.160099838533	-0.371830570077	0.105778332535	0.111267228627	0.386994041955	-0.0143724235093	-0.0768387573568	0.349887706097	0.134607833371	0.397125488598	44.396611331	93.8841392443	64.2473320926
18	0.848750807453	-0.164600353126	-0.087971891862	2.03937275489	-0.00222645134928	1.79851769211	0.084202232599	0.228850765205	0.359878753162	-0.168094855321	-0.0759997495916	0.0658840297992	-0.340923388384	0.339135579519	0.136625788295	0.26344879071	-0.00530868012889	-0.0214475554232	0.426526662316	0.087580819495	0.337862401001	48.9300611487	83.6200265732	62.3680065569
19	1.58011760728	-0.362164237169	0.663740156871	2.2612891254	-0.0939536703742	1.07229069083	-0.090844539294	0.200961705548	0.0171228241352	-0.10240265202	-0.0868899702359	-0.259410294146	-0.0548158511388	0.415836878784	0.0998072847929	0.257698853555	-0.0200894211403	-0.00514454494066	0.536735616884	0.0851867421516	0.388328810595	60.7943384081	76.8996012195	66.0120010324
20	1.35820542889	-0.0651154940881	-0.100623967837	1.33506609088	0.0188802497768	1.28806115546	-0.0373097843718	-0.013553682339	0.160381071361	0.0187120952597	-0.0683959150758	-0.233159928676	-0.196696037913	0.460703510759	0.0418082935119	0.349319167543	-0.121265828394	-0.0649853487132	0.456833590278	0.116023063675	0.390213179858	62.4412446635	91.9859814882	77.2083451766
21	0.844300440849	0.254504465714	-0.555969748295	1.40338721842	0.149611570383	1.29445412593	-0.0134084458447	-0.00419994120142	0.736777804817	-0.0835914627049	0.050884407102	-0.395637752283	-0.507167477712	0.49866305285	0.0311999324135	0.512882388915	-0.244160190518	-0.0775105095519	0.53712225038	0.173040773994	0.535323671899	65.0052619688	102.845536805	72.7904778576
22	0.420964491508	-0.371892397796	-0.209969838135	0.707425887665	-0.121582176793	0.573551127715	-0.184679372285	0.732907290543	0.444307333532	-0.789601310496	0.0880485646816	0.426051425299	-0.237508335691	-0.0439802130248	0.0242428325439	0.549697191702	0.0320144700747	-0.209471283631	0.36544909505	0.178548509519	0.651272549098	27.9345479416	99.1854719017	64.5215412534
23	1.01244038283	0.745232510002	-0.252686129912	0.926951823065	0.204971986165	1.08315757259	-0.0570157395086	0.0595520477899	0.327610471137	0.0728556204766	-0.0252719152717	0.231760438417	-0.257088785479	-0.0997327777883	0.0891393189841	0.407036747911	0.0597983038375	-0.0870853595807	0.288306549569	0.0535015674522	0.534069452013	27.4118331536	96.7062635286	75.8872113875
24	1.69350921205	-0.622740127124	0.262017505502	2.35172092579	-0.158447921079	2.50929862406	-0.0633794814531	-0.265319842145	0.429276482426	0.198548203426	0.0223835994305	0.610812487241	-0.258860035951	-0.340672208341	0.145300037438	0.365331148921	0.0528591565337	-0.0139357417417	0.261019876745	-0.0408278460864	0.54461976859	21.2344308823	95.2969266654	84.3424530114
25	0.664230408314	0.194033633876	0.518064535954	1.64305929035	0.317188764866	1.7091714937	-0.202437585145	-0.0599511342369	0.620575828041	0.0914020967974	-0.0248292619257	0.173207705423	-0.488084405514	-0.130332219176	0.154083127887	0.478123247596	0.0272402045125	-0.0628331654903	0.292069818589	0.0177942767814	0.536475118628	29.9993523232	100.171963271	81.5027612171

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 128 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 129 through 188 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 189 through 305 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 306 through 399 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 400 through 440 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 441 through 536 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 67 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 68 through 156 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 157 through 289 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 290 through 330 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 331 through 440 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 441 through 536 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1 through 128 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 129 through 258 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 259 through 536 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 28 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 29 through 67 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 68 through 128 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 129 through 188 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 189 through 289 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 290 through 330 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 331 through 368 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 369 through 405 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 406 through 461 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 462 through 536 )

-
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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi