PDB-8csf: WbbB D232C-Kdo adduct + alpha-Rha(1,3)GlcNAc ternary complex

ID or keywords:

Entry

Database: PDB / ID: 8csf

Title

WbbB D232C-Kdo adduct + alpha-Rha(1,3)GlcNAc ternary complex

Components

N-acetyl glucosaminyl transferase

Keywords

TRANSFERASE / Glycsoyltransferase / retaining / ternary complex

Function / homology

Capsule polysaccharide biosynthesis / Capsule polysaccharide biosynthesis protein / polysaccharide transport / polysaccharide biosynthetic process / transferase activity / CYTIDINE-5'-MONOPHOSPHATE / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / Putative N-acetyl glucosaminyl transferase

Function and homology information

Biological species

Raoultella terrigena (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Forrester, T.J.B. / Kimber, M.S.

Funding support

Canada, 1items

Citation

Journal: Nat Commun / Year: 2022
Title: The retaining beta-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step.
Authors: Forrester, T.J.B. / Ovchinnikova, O.G. / Li, Z. / Kitova, E.N. / Nothof, J.T. / Koizumi, A. / Klassen, J.S. / Lowary, T.L. / Whitfield, C. / Kimber, M.S.

History

Deposition	May 12, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2022	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
Revision 1.2	Nov 15, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8csf.cif.gz	405.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8csf.ent.gz	275.8 KB	Display	PDB format
PDBx/mmJSON format	8csf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8csf_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	8csf_full_validation.pdf.gz	2.4 MB	Display
Data in XML	8csf_validation.xml.gz	19.4 KB	Display
Data in CIF	8csf_validation.cif.gz	29.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cs/8csf ftp://data.pdbj.org/pub/pdb/validation_reports/cs/8csf	HTTPS FTP

-
Related structure data

Related structure data	8csbC 8cscC 8csdC 8cseC 5fa1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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: N-acetyl glucosaminyl transferase

B: N-acetyl glucosaminyl transferase

hetero molecules

94.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N-acetyl glucosaminyl transferase

hetero molecules

A: N-acetyl glucosaminyl transferase

hetero molecules

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

2

B: N-acetyl glucosaminyl transferase

hetero molecules

B: N-acetyl glucosaminyl transferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	92.500, 158.070, 116.680
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

-
Protein , 1 types, 2 molecules AB

#1: Protein	N-acetyl glucosaminyl transferase / retaining Kdo transferase Mass: 46116.824 Da / Num. of mol.: 2 / Mutation: D232C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Raoultella terrigena (bacteria) / Gene: wbbB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q6U8B0

-
Sugars , 2 types, 4 molecules

#2: Polysaccharide

alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
LRhapa1-3DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2211m-1a_1-5]/1-2/a3-b1	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][a-L-Rhap]{}}	LINUCS	PDB-CARE

#5: Sugar

ChemComp-KDO / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / 3-deoxy-d-manno-oct-2-ulopyranosonic acid / 2-keto-3-deoxy-D-mannooctanoic acid / 3-deoxy-alpha-D-manno-oct-2-ulosonic acid / 3-deoxy-D-manno-oct-2-ulosonic acid / 3-deoxy-manno-oct-2-ulosonic acid

Type: D-saccharide, alpha linking / Mass: 238.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₄O₈ / Feature type: SUBJECT OF INVESTIGATION

-
Non-polymers , 3 types, 256 molecules

#3: Chemical	ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₄N₃O₈P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.26 % / Description: prisms
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.1 M sodium malonate, 100 mM HEPES, and 0.5 % Jeffamine ED-2001

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 6, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.4→46 Å / Num. obs: 33794 / % possible obs: 99.9 % / Redundancy: 7.5 % / B_iso Wilson estimate: 45.73 Å² / R_sym value: 0.088 / Net I/σ(I): 16.74
Reflection shell	Resolution: 2.4→2.5 Å / Mean I/σ(I) obs: 2.11 / Num. unique obs: 3850 / CC_1/2: 0.78 / R_sym value: 0.96 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FA1

5fa1

Resolution: 2.4→45.78 Å / SU ML: 0.2611 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7524
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2213	1687	5 %
R_work	0.1723	32085	-
obs	0.1748	33772	99.88 %

Solvent computation

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

Displacement parameters

B_iso mean: 51.11 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→45.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6189	0	126	250	6565

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0076	6486
X-RAY DIFFRACTION	f_angle_d	0.9691	8822
X-RAY DIFFRACTION	f_chiral_restr	0.0515	997
X-RAY DIFFRACTION	f_plane_restr	0.0069	1124
X-RAY DIFFRACTION	f_dihedral_angle_d	20.9979	2280

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 (%)
2.4-2.47	0.2778	140	0.2196	2665	X-RAY DIFFRACTION	99.96
2.47-2.55	0.295	139	0.2166	2631	X-RAY DIFFRACTION	99.93
2.55-2.64	0.2616	138	0.211	2638	X-RAY DIFFRACTION	99.86
2.64-2.75	0.281	139	0.2042	2654	X-RAY DIFFRACTION	99.96
2.75-2.87	0.2513	139	0.2124	2638	X-RAY DIFFRACTION	100
2.87-3.02	0.2488	139	0.1947	2644	X-RAY DIFFRACTION	99.86
3.02-3.21	0.2808	139	0.1954	2657	X-RAY DIFFRACTION	99.89
3.21-3.46	0.2305	141	0.1804	2673	X-RAY DIFFRACTION	99.93
3.46-3.81	0.2254	141	0.1641	2687	X-RAY DIFFRACTION	99.89
3.81-4.36	0.1816	141	0.1438	2680	X-RAY DIFFRACTION	99.79
4.36-5.49	0.2213	142	0.1469	2711	X-RAY DIFFRACTION	99.93
5.49-45.78	0.1781	149	0.1655	2807	X-RAY DIFFRACTION	99.53

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	3.96877112227	0.117859917703	1.34531921438	4.52995936826	1.71711900416	1.80276013013	0.179619697694	-0.382821569135	-0.389375049426	0.29329202619	-0.119592331554	-0.0179663666767	0.326557253378	-0.041012435561	-0.0446449756725	0.482243298936	-0.0734256650489	-0.110010957343	0.410326233242	0.0458448258023	0.267142753819	17.5688594522	15.5383710129	43.2327163687
2	0.752838328821	-0.468416334005	-0.383561126056	3.15992061856	1.4624120112	2.52841367863	0.397961513516	-0.279011366407	-0.236816391627	0.521259117772	-0.054320796184	-0.774006445834	0.578258460368	0.147551849127	0.138762937717	0.539487513282	0.0438702930271	-0.254451332125	0.45922537007	0.0458780272834	0.66983474599	29.2514802926	12.1528840736	43.6852733965
3	2.56899436169	1.02802228365	-0.659902790147	4.03068255037	-4.28820092068	4.73962469655	-0.0385558116725	-1.39931279289	-1.18792764676	1.6093119766	0.341037292305	0.467288607483	2.15037964715	-0.188133796355	0.191019064098	1.29686636773	-0.140418249814	-0.125963487982	0.845022741189	0.132080857827	0.561891425662	19.5898986601	8.8944337384	52.0897168663
4	1.59690457761	0.26498588754	0.924756736607	1.02703719312	0.423846848509	0.910013173806	0.234195040194	-0.437213087301	-0.445429353566	0.842586283467	-0.118672757898	-0.220021358056	0.635875385417	0.116880874521	0.0723893447525	0.812160242766	-0.015445129461	-0.133863569033	0.545712956875	0.0868852115353	0.593892259841	20.7456557671	10.3296491512	46.6561842684
5	2.85221145805	0.25089059953	-0.410773842997	4.63691240519	0.57649588632	3.72588068515	0.134356736211	-0.240016422203	0.166451583787	0.459617453557	-0.087046131152	-0.220540424634	0.0102687200461	-0.120008545108	-0.133342339614	0.345366721862	-0.0299672048309	-0.0395697158313	0.244240163915	0.0358978019981	0.268464941419	18.8966155074	26.1136231918	43.3553078927
6	0.500042998612	0.923101485467	-0.271979348387	2.60251138286	2.56643164324	2.79022662869	0.182149299531	0.0571804044303	-0.069592639464	0.175851864405	-0.00884998966856	-0.73915136515	0.193904084322	0.0648344114898	0.0899526968663	0.359002243332	0.0563369643612	-0.0708011271758	0.315249420828	0.0373905555602	0.415058687857	24.7435630679	19.2486887715	30.8745274159
7	0.994381780931	-0.655257140422	0.266733385562	1.75961138496	2.3870123707	3.90155483181	-0.00934766395091	0.384181992367	-0.0727819340055	-0.814139203745	0.168168689955	-0.303969559084	-0.370690278824	-0.043346161508	0.102658479149	0.537129020976	0.0700204491541	0.0694451348876	0.473871277093	-0.0546507472549	0.50455988569	26.4377475354	9.59220017977	11.8094906184
8	4.21349518179	-0.84023491391	-1.21543191003	3.847867284	0.980129431546	3.01340165068	0.0627725314187	0.32886926373	-0.418382631321	-0.025674087196	-0.188207616188	0.459241707015	0.144013193701	-0.344970876609	-0.215380197384	0.392824285966	0.0346956967361	-0.0269715853127	0.352208047686	-0.00699717485336	0.362553375401	3.88583801341	6.86916233282	20.9975769105
9	3.29744453125	0.841350877498	-0.053196540437	3.00993777807	0.576986753292	1.84128812105	0.0861105232862	0.304396944027	0.0158418471637	-0.439107665417	0.0104913453347	-0.150829637985	-0.101767338345	-0.0851374106576	0.134288128006	0.429478791504	0.0934484816235	0.0210251068057	0.313267128863	0.013114879058	0.30497427578	17.6988702928	11.5514958356	13.9432272666
10	1.28638201091	0.680990894211	0.0131997940329	1.63522394581	1.19297611652	5.52152602428	0.0515599626105	0.136779341782	-0.254546192419	0.0136600012031	0.305170400195	-1.34292843654	-0.00953674396432	0.874953893534	0.312553690034	0.350618522707	0.1070431743	-0.0257249688471	0.477397004949	-0.107539598888	0.808584038304	36.6663569357	15.8722999636	27.036321909
11	4.13035012784	-0.411681090903	-2.04591145392	4.51392183541	1.372305271	5.95754751344	0.301376685472	1.27481070958	-0.685975959604	-0.592083974983	-0.175132572074	-2.22999920696	0.687467244859	0.998316601512	0.439260784221	0.722950903028	0.273427939283	0.16823891746	0.908043986349	-0.0688929827683	0.841835345857	39.2910495544	10.4194938713	11.5499172586
12	2.2000115221	2.81154911069	0.222258482721	4.04609588072	-0.334333966079	3.58994556087	0.237827576143	0.98181675778	0.031231814799	-0.108234902908	-0.185278859836	-0.213167516699	0.495325870233	0.577840001122	-0.010973411777	0.366748168933	0.116507991136	0.0281191356724	0.441362902689	-0.0702214318586	0.358971924108	31.259404476	45.0346530529	25.5447562604
13	4.35093671192	1.19377073814	0.727236622899	6.20901585834	1.32363809462	4.30569895301	0.164942858772	0.55257683471	-0.134727519862	-0.736715381498	-0.232459201562	0.242006224086	-0.28757405737	-0.179802061864	-0.27210720907	0.400537593092	0.019705915647	0.0159971077635	0.388802739829	0.0374420575704	0.325943674298	17.7278653738	51.5030720248	19.9822087466
14	1.82826967393	-2.15177674372	1.1833858744	3.25825996198	0.0585648085186	3.67406887685	-0.251119554461	0.502251423287	-0.0824718814897	-0.198406825737	0.181680856694	-0.393453700501	-0.481420884627	0.725927650981	0.00419986734167	0.432001485766	-0.108155365446	0.00326205820273	0.532787213594	-0.0347413335529	0.4166232362	29.0073400816	56.130030335	25.4861339087
15	4.05296205214	3.7703966328	3.46083862394	3.79953268267	1.97619451515	7.26968617281	0.238790983663	0.655654297125	0.725855214499	-0.628138487514	0.217688817553	-1.38767419101	-0.12172026678	1.86100117266	-0.197156808299	0.339946939594	-0.0635891370114	0.0756643456686	0.66629824521	0.0732624255865	0.943450814023	38.885889049	53.5421684636	26.7274360376
16	5.87502050155	1.60557392118	-1.97842924851	6.29370589695	2.49044144668	4.63647640367	0.0693946025307	0.320027787034	-0.0236692100123	-1.40575798277	-0.32079549345	-0.163603559098	0.203785694744	0.270516852597	0.101694750571	0.413578487094	0.0737392402458	0.0789666686963	0.46177256159	-0.0113823987602	0.423093749653	30.1073956198	47.0826193399	19.7064792739
17	3.12841515035	-0.519557046528	-1.26449568543	6.24894550677	-2.12419473893	7.31161734928	-0.251434559537	0.984970942769	0.0914349240882	-2.22706712267	-0.0063655053371	0.362210516692	-1.68101277057	1.20436087303	-0.243808427301	0.88838393559	-0.0616745602707	0.0551214436469	0.778310132284	0.0820760933911	0.506659135485	25.5906824471	56.6334406849	13.4880689663
18	3.51366153415	-0.137170693341	-0.297216242235	1.75096534926	2.77121935178	4.69829287289	-0.0226400479004	0.565604640479	0.690704005507	-0.729315916333	-0.14537530741	-0.387540527672	-0.735842383162	0.459038187618	-0.240602640741	0.76760223378	-0.128380584624	0.0449149965592	0.471650134005	0.105764911963	0.612522860783	28.1901875201	63.9167151076	22.593971265
19	7.10603626147	1.64432343067	0.691890321637	4.58335928524	-0.119669513212	3.40595323344	-0.16385593132	1.15993725292	-0.527742252959	-0.870761366314	-0.047071481184	-0.244833348694	0.0149864613173	0.405393776553	-0.00553431536965	0.514226921138	0.0913799405462	0.0407397903826	0.489370642065	-0.042983290163	0.322260300039	21.4432460546	44.4316856225	14.7466154285
20	3.82205784586	-1.59885324286	0.781733193209	3.36939991334	-0.92342871326	4.37135252864	0.448656106229	0.39023126931	-0.732567999131	-0.455034118006	0.105229805374	0.732378734622	0.785998289094	-0.597925477916	-0.283063148991	0.308331058414	0.0104844701427	-0.0511119746085	0.362033499534	0.00346223307552	0.357341665217	8.77672682147	43.5743431397	21.9280339081
21	2.48974359382	-0.396782859106	-0.60587289577	4.47182689764	1.08795521365	4.54651053782	0.233732350273	0.866004062584	-0.68598786553	-0.367662871929	-0.262883153598	-0.608446959088	0.0781080723463	0.369024557343	0.0509393262026	0.494553427849	0.0710377554268	0.0153729662418	0.421474124533	-0.0266041326743	0.403890604009	28.1012838015	35.7094189117	18.5231686221
22	3.2043715486	-2.20642267008	-0.346059134094	4.01101038239	0.897960892647	3.30372376684	0.0656237762498	-0.169387870855	-0.29426927461	-0.0934592246481	0.137588791641	-0.259321137102	0.199930635609	0.142783790225	0.0947323120545	0.304381589598	0.0339442207956	0.0085700388343	0.284621808654	0.0107648255545	0.382022376641	26.2030001114	38.1120242525	27.716940982
23	0.500968971705	-1.29454379309	-0.11317610011	1.62268373109	0.724430121423	2.09684730575	0.0485205049333	0.0749714887058	0.0455435625011	0.0235898544195	0.0241052191551	-0.341432707632	-0.157328470537	0.124802268391	0.0417915709627	0.305096487742	-0.0491101737438	-0.050784034933	0.268387007915	-0.0035157417446	0.354888050156	23.7230809162	50.1635466062	37.9371443844
24	2.99414135147	-0.199313791832	-0.561992123489	3.84745998	1.45422212362	3.71624353435	-0.209699710417	-0.60549612979	-0.0136298975278	0.785835414274	0.175758601218	0.0413234845704	-0.00988130935987	-0.0743558535155	-0.242395416862	0.426327715982	-0.0539157511184	-0.037744552984	0.476487082986	-0.0293885147559	0.349149818935	22.454845399	54.1013789575	53.6290843614
25	4.54325655451	-0.333300986445	-0.120922191141	2.45915356015	-0.381076492094	4.05821072529	0.0848547963172	-0.136563953723	0.0372191954228	0.0173608010523	-0.0113631787548	0.142868781876	0.0268218374986	-0.0536866756822	0.0284975626455	0.321674250519	-0.0310243987823	-0.0563469479321	0.269283861033	-0.000104503497219	0.28236148822	2.52528923951	53.2395473193	38.100772976
26	1.80756723525	0.279987688902	-0.487459516893	3.09911533254	-0.479493765814	5.57434086918	0.0758143632337	0.0799234737782	0.121514532953	-0.07975161372	-0.0238877157409	0.712386920077	-0.495875498852	-0.668003003665	-0.402156054376	0.387516377252	0.035699513516	-0.0437454274458	0.324170789635	-0.0225010590261	0.497479398151	-0.91601602199	62.5017575923	39.2819394082
27	3.98241809385	0.236382314229	0.601091495123	2.97709425567	0.131870675265	5.83384689236	-0.0500550996437	0.961458698149	0.800714838062	-0.822109673172	-0.652831602395	0.852708679658	-1.49894517947	-0.820658294699	0.140661512557	0.529862271885	0.234608528956	-0.0630512553517	0.638491597417	-0.156360525473	0.5405285548	0.364709707091	68.9289245404	39.5920483603
28	1.27281623903	0.427590678757	0.25048391606	1.84052343511	0.0469500241599	1.97509653652	-0.0479148431514	-0.302620656409	0.0868776508	0.27372721399	-0.038487584897	-0.0363991331976	0.0585120266345	-0.0720701604219	-0.021099765244	0.36691872257	-0.0409849583232	-0.0639483707879	0.344827887465	-0.0150496063352	0.312805702805	15.3673133323	53.706655456	47.5120467012
29	3.57535913039	-1.15008871941	-0.0904461700925	3.82653795916	2.60225378975	7.80728756865	0.0945282121193	-0.315306060006	-0.237310724261	0.137109560707	0.0100286560939	-1.38837451669	-0.118547306323	0.602090900165	0.00109068281756	0.242040863282	-0.0518196024668	-0.102187044756	0.454471478292	-0.0244326955543	0.566928208155	35.9479659748	48.9767663213	44.1520137523
30	3.94315003775	1.24519172332	0.293400170982	9.75150814455	0.216100213448	9.27854612125	-0.383900552519	-0.63677955817	1.03465016019	1.38316980782	0.435482475533	-1.44034062623	0.0594891663816	0.949457380998	-0.118953333772	0.525168992945	-0.0600533758352	-0.173714554484	0.715674787656	-0.0424339964815	0.653455824233	32.4762518139	56.8989570449	58.2503802868

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 18 )	A	A	1 - 18	1 - 18
2	2	chain 'A' and (resid 19 through 38 )	A	A	19 - 38	19 - 38
3	3	chain 'A' and (resid 39 through 46 )	A	A	39 - 46	39 - 46
4	4	chain 'A' and (resid 49 through 94 )	A	A	49 - 94	47 - 92
5	5	chain 'A' and (resid 95 through 140 )	A	A	95 - 140	93 - 138
6	6	chain 'A' and (resid 141 through 183 )	A	A	141 - 183	139 - 181
7	7	chain 'A' and (resid 184 through 222 )	A	A	184 - 222	182 - 220
8	8	chain 'A' and (resid 223 through 284 )	A	A	223 - 284	221 - 282
9	9	chain 'A' and (resid 285 through 342 )	A	A	285 - 342	283 - 340
10	10	chain 'A' and (resid 343 through 379 )	A	A	343 - 379	341 - 377
11	11	chain 'A' and (resid 391 through 403 )	A	A	391 - 403	378 - 390
12	12	chain 'B' and (resid 1 through 5 )	B	B	1 - 5	1 - 5
13	13	chain 'B' and (resid 6 through 18 )	B	B	6 - 18	6 - 18
14	14	chain 'B' and (resid 19 through 26 )	B	B	19 - 26	19 - 26
15	15	chain 'B' and (resid 27 through 33 )	B	B	27 - 33	27 - 33
16	16	chain 'B' and (resid 34 through 38 )	B	B	34 - 38	34 - 38
17	17	chain 'B' and (resid 39 through 46 )	B	B	39 - 46	39 - 46
18	18	chain 'B' and (resid 49 through 75 )	B	B	49 - 75	47 - 73
19	19	chain 'B' and (resid 76 through 94 )	B	B	76 - 94	74 - 92
20	20	chain 'B' and (resid 95 through 107 )	B	B	95 - 107	93 - 105
21	21	chain 'B' and (resid 108 through 130 )	B	B	108 - 130	106 - 128
22	22	chain 'B' and (resid 131 through 150 )	B	B	131 - 150	129 - 148
23	23	chain 'B' and (resid 151 through 183 )	B	B	151 - 183	149 - 181
24	24	chain 'B' and (resid 184 through 216 )	B	B	184 - 216	182 - 214
25	25	chain 'B' and (resid 220 through 253 )	B	B	220 - 253	215 - 248
26	26	chain 'B' and (resid 254 through 273 )	B	B	254 - 273	249 - 268
27	27	chain 'B' and (resid 274 through 284 )	B	B	274 - 284	269 - 279
28	28	chain 'B' and (resid 285 through 353 )	B	B	285 - 353	280 - 348
29	29	chain 'B' and (resid 354 through 380 )	B	B	354 - 380	349 - 375
30	30	chain 'B' and (resid 390 through 405 )	B	B	390 - 405	376 - 391

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Sugars , 2 types, 4 molecules

-
Non-polymers , 3 types, 256 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, 2 molecules AB

-Sugars , 2 types, 4 molecules

-Non-polymers , 3 types, 256 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, 2 molecules AB

-
Sugars , 2 types, 4 molecules

-
Non-polymers , 3 types, 256 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