[English] 日本語
Yorodumi
- PDB-6hnq: TarP-6RboP-(CH2)6NH2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hnq
TitleTarP-6RboP-(CH2)6NH2
ComponentsProbable ss-1,3-N-acetylglucosaminyltransferase
KeywordsTRANSFERASE / Staphylococcus aureus / wall teichoic acid / glycosyltransferase / GT-A fold
Function / homology
Function and homology information


teichoic acid biosynthetic process / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cell wall organization / metal ion binding
Similarity search - Function
Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Chem-FQ8 / Poly(ribitol-phosphate) beta-N-acetylglucosaminyltransferase TarP
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsGuo, Y. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationTRR34, CRC766 Germany
CitationJournal: Nature / Year: 2018
Title: Methicillin-resistant Staphylococcus aureus alters cell wall glycosylation to evade immunity.
Authors: Gerlach, D. / Guo, Y. / De Castro, C. / Kim, S.H. / Schlatterer, K. / Xu, F.F. / Pereira, C. / Seeberger, P.H. / Ali, S. / Codee, J. / Sirisarn, W. / Schulte, B. / Wolz, C. / Larsen, J. / ...Authors: Gerlach, D. / Guo, Y. / De Castro, C. / Kim, S.H. / Schlatterer, K. / Xu, F.F. / Pereira, C. / Seeberger, P.H. / Ali, S. / Codee, J. / Sirisarn, W. / Schulte, B. / Wolz, C. / Larsen, J. / Molinaro, A. / Lee, B.L. / Xia, G. / Stehle, T. / Peschel, A.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Probable ss-1,3-N-acetylglucosaminyltransferase
C: Probable ss-1,3-N-acetylglucosaminyltransferase
F: Probable ss-1,3-N-acetylglucosaminyltransferase
O: Probable ss-1,3-N-acetylglucosaminyltransferase
P: Probable ss-1,3-N-acetylglucosaminyltransferase
E: Probable ss-1,3-N-acetylglucosaminyltransferase
G: Probable ss-1,3-N-acetylglucosaminyltransferase
Q: Probable ss-1,3-N-acetylglucosaminyltransferase
A: Probable ss-1,3-N-acetylglucosaminyltransferase
D: Probable ss-1,3-N-acetylglucosaminyltransferase
H: Probable ss-1,3-N-acetylglucosaminyltransferase
I: Probable ss-1,3-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)487,28845
Polymers478,66412
Non-polymers8,62433
Water25,8701436
1
B: Probable ss-1,3-N-acetylglucosaminyltransferase
C: Probable ss-1,3-N-acetylglucosaminyltransferase
F: Probable ss-1,3-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,88413
Polymers119,6663
Non-polymers2,21810
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-95 kcal/mol
Surface area38860 Å2
MethodPISA
2
O: Probable ss-1,3-N-acetylglucosaminyltransferase
H: Probable ss-1,3-N-acetylglucosaminyltransferase
I: Probable ss-1,3-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,81311
Polymers119,6663
Non-polymers2,1478
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-80 kcal/mol
Surface area38810 Å2
MethodPISA
3
P: Probable ss-1,3-N-acetylglucosaminyltransferase
A: Probable ss-1,3-N-acetylglucosaminyltransferase
D: Probable ss-1,3-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,77810
Polymers119,6663
Non-polymers2,1127
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-64 kcal/mol
Surface area39230 Å2
MethodPISA
4
E: Probable ss-1,3-N-acetylglucosaminyltransferase
G: Probable ss-1,3-N-acetylglucosaminyltransferase
Q: Probable ss-1,3-N-acetylglucosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,81311
Polymers119,6663
Non-polymers2,1478
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-76 kcal/mol
Surface area38610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.410, 211.250, 122.680
Angle α, β, γ (deg.)90.00, 91.61, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
12B
22F
13B
23O
14B
24P
15B
25E
16B
26G
17B
27Q
18B
28A
19B
29D
110B
210H
111B
211I
112C
212F
113C
213O
114C
214P
115C
215E
116C
216G
117C
217Q
118C
218A
119C
219D
120C
220H
121C
221I
122F
222O
123F
223P
124F
224E
125F
225G
126F
226Q
127F
227A
128F
228D
129F
229H
130F
230I
131O
231P
132O
232E
133O
233G
134O
234Q
135O
235A
136O
236D
137O
237H
138O
238I
139P
239E
140P
240G
141P
241Q
142P
242A
143P
243D
144P
244H
145P
245I
146E
246G
147E
247Q
148E
248A
149E
249D
150E
250H
151E
251I
152G
252Q
153G
253A
154G
254D
155G
255H
156G
256I
157Q
257A
158Q
258D
159Q
259H
160Q
260I
161A
261D
162A
262H
163A
263I
164D
264H
165D
265I
166H
266I

NCS domain segments:

Component-ID: _ / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETBA1 - 32719 - 345
21METMETCB1 - 32719 - 345
12METMETBA1 - 32619 - 344
22METMETFC1 - 32619 - 344
13METMETBA1 - 32719 - 345
23METMETOD1 - 32719 - 345
14METMETBA1 - 32719 - 345
24METMETPE1 - 32719 - 345
15SERSERBA0 - 32718 - 345
25SERSEREF0 - 32718 - 345
16METMETBA1 - 32719 - 345
26METMETGG1 - 32719 - 345
17METMETBA1 - 32719 - 345
27METMETQH1 - 32719 - 345
18SERSERBA0 - 32718 - 345
28SERSERAI0 - 32718 - 345
19METMETBA1 - 32719 - 345
29METMETDJ1 - 32719 - 345
110SERSERBA0 - 32718 - 345
210SERSERHK0 - 32718 - 345
111METMETBA1 - 32719 - 345
211METMETIL1 - 32719 - 345
112METMETCB1 - 32719 - 345
212METMETFC1 - 32719 - 345
113METMETCB1 - 32719 - 345
213METMETOD1 - 32719 - 345
114METMETCB1 - 32619 - 344
214METMETPE1 - 32619 - 344
115METMETCB1 - 32719 - 345
215METMETEF1 - 32719 - 345
116METMETCB1 - 32719 - 345
216METMETGG1 - 32719 - 345
117METMETCB1 - 32719 - 345
217METMETQH1 - 32719 - 345
118METMETCB1 - 32719 - 345
218METMETAI1 - 32719 - 345
119METMETCB1 - 32719 - 345
219METMETDJ1 - 32719 - 345
120METMETCB1 - 32719 - 345
220METMETHK1 - 32719 - 345
121METMETCB1 - 32719 - 345
221METMETIL1 - 32719 - 345
122METMETFC1 - 32719 - 345
222METMETOD1 - 32719 - 345
123METMETFC1 - 32719 - 345
223METMETPE1 - 32719 - 345
124METMETFC1 - 32719 - 345
224METMETEF1 - 32719 - 345
125METMETFC1 - 32719 - 345
225METMETGG1 - 32719 - 345
126METMETFC1 - 32719 - 345
226METMETQH1 - 32719 - 345
127METMETFC1 - 32719 - 345
227METMETAI1 - 32719 - 345
128METMETFC1 - 32719 - 345
228METMETDJ1 - 32719 - 345
129METMETFC1 - 32619 - 344
229METMETHK1 - 32619 - 344
130METMETFC1 - 32719 - 345
230METMETIL1 - 32719 - 345
131METMETOD1 - 32719 - 345
231METMETPE1 - 32719 - 345
132METMETOD1 - 32619 - 344
232METMETEF1 - 32619 - 344
133METMETOD1 - 32719 - 345
233METMETGG1 - 32719 - 345
134METMETOD1 - 32719 - 345
234METMETQH1 - 32719 - 345
135METMETOD1 - 32619 - 344
235METMETAI1 - 32619 - 344
136METMETOD1 - 32719 - 345
236METMETDJ1 - 32719 - 345
137METMETOD1 - 32719 - 345
237METMETHK1 - 32719 - 345
138METMETOD1 - 32719 - 345
238METMETIL1 - 32719 - 345
139METMETPE1 - 32619 - 344
239METMETEF1 - 32619 - 344
140METMETPE1 - 32619 - 344
240METMETGG1 - 32619 - 344
141METMETPE1 - 32619 - 344
241METMETQH1 - 32619 - 344
142METMETPE1 - 32619 - 344
242METMETAI1 - 32619 - 344
143METMETPE1 - 32619 - 344
243METMETDJ1 - 32619 - 344
144METMETPE1 - 32719 - 345
244METMETHK1 - 32719 - 345
145METMETPE1 - 32619 - 344
245METMETIL1 - 32619 - 344
146METMETEF1 - 32719 - 345
246METMETGG1 - 32719 - 345
147METMETEF1 - 32719 - 345
247METMETQH1 - 32719 - 345
148SERSEREF0 - 32718 - 345
248SERSERAI0 - 32718 - 345
149METMETEF1 - 32719 - 345
249METMETDJ1 - 32719 - 345
150SERSEREF0 - 32718 - 345
250SERSERHK0 - 32718 - 345
151METMETEF1 - 32719 - 345
251METMETIL1 - 32719 - 345
152METMETGG1 - 32719 - 345
252METMETQH1 - 32719 - 345
153METMETGG1 - 32719 - 345
253METMETAI1 - 32719 - 345
154METMETGG1 - 32719 - 345
254METMETDJ1 - 32719 - 345
155METMETGG1 - 32719 - 345
255METMETHK1 - 32719 - 345
156METMETGG1 - 32719 - 345
256METMETIL1 - 32719 - 345
157METMETQH1 - 32719 - 345
257METMETAI1 - 32719 - 345
158METMETQH1 - 32719 - 345
258METMETDJ1 - 32719 - 345
159METMETQH1 - 32719 - 345
259METMETHK1 - 32719 - 345
160METMETQH1 - 32719 - 345
260METMETIL1 - 32719 - 345
161METMETAI1 - 32719 - 345
261METMETDJ1 - 32719 - 345
162SERSERAI0 - 32718 - 345
262SERSERHK0 - 32718 - 345
163METMETAI1 - 32719 - 345
263METMETIL1 - 32719 - 345
164METMETDJ1 - 32719 - 345
264METMETHK1 - 32719 - 345
165METMETDJ1 - 32719 - 345
265METMETIL1 - 32719 - 345
166METMETHK1 - 32719 - 345
266METMETIL1 - 32719 - 345

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

-
Components

#1: Protein
Probable ss-1,3-N-acetylglucosaminyltransferase / TarP-6RboP-(CH2)6NH2


Mass: 39888.680 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Gene: SA1808 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JNB0
#2: Chemical
ChemComp-FQ8 / [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] [(2~{R},3~{R},4~{S})-2,3,4-tris(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentoxy]phosphoryl]oxy-pentyl] hydrogen phosphate


Mass: 660.346 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C15H35O22P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1436 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 250 mM magnesium chloride, 0.1 M sodium citrate, pH 5.7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.4→48.5 Å / Num. obs: 188717 / % possible obs: 99.9 % / Redundancy: 6.2 % / Net I/σ(I): 10.84
Reflection shellResolution: 2.4→2.46 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.4→48.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 18.836 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22781 9436 5 %RANDOM
Rwork0.18372 ---
obs0.18593 179281 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.749 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å2-0.45 Å2
2--0.27 Å20 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.4→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29279 0 501 1436 31216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01330238
X-RAY DIFFRACTIONr_bond_other_d0.0020.01727344
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.66140837
X-RAY DIFFRACTIONr_angle_other_deg1.4121.59963355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59753745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51523.9121411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.993155259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.93715104
X-RAY DIFFRACTIONr_chiral_restr0.0610.24233
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0233238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026070
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.64311.03115060
X-RAY DIFFRACTIONr_mcbond_other5.64311.03115059
X-RAY DIFFRACTIONr_mcangle_it7.53114.83918775
X-RAY DIFFRACTIONr_mcangle_other7.53114.83918776
X-RAY DIFFRACTIONr_scbond_it7.04111.92615178
X-RAY DIFFRACTIONr_scbond_other7.03711.92615178
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.3215.61422062
X-RAY DIFFRACTIONr_long_range_B_refined11.45862.008127595
X-RAY DIFFRACTIONr_long_range_B_other11.45961.892127070
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B102960.07
12C102960.07
21B104560.07
22F104560.07
31B105080.06
32O105080.06
41B81970.08
42P81970.08
51B105070.06
52E105070.06
61B104070.06
62G104070.06
71B92580.09
72Q92580.09
81B104550.06
82A104550.06
91B104740.06
92D104740.06
101B107730.05
102H107730.05
111B102760.07
112I102760.07
121C102890.06
122F102890.06
131C103000.05
132O103000.05
141C81900.09
142P81900.09
151C102810.06
152E102810.06
161C103710.05
162G103710.05
171C92600.07
172Q92600.07
181C102430.06
182A102430.06
191C103120.06
192D103120.06
201C102880.07
202H102880.07
211C102870.06
212I102870.06
221F106040.06
222O106040.06
231F82120.09
232P82120.09
241F104370.07
242E104370.07
251F104280.06
252G104280.06
261F92910.08
262Q92910.08
271F104220.07
272A104220.07
281F104540.07
282D104540.07
291F104580.07
292H104580.07
301F103120.06
302I103120.06
311O82340.08
312P82340.08
321O103920.06
322E103920.06
331O104060.05
332G104060.05
341O93220.08
342Q93220.08
351O103740.06
352A103740.06
361O104930.05
362D104930.05
371O105100.06
372H105100.06
381O103300.06
382I103300.06
391P81370.09
392E81370.09
401P81860.09
402G81860.09
411P81340.09
412Q81340.09
421P80950.09
422A80950.09
431P81840.08
432D81840.08
441P81860.09
442H81860.09
451P81810.08
452I81810.08
461E103890.06
462G103890.06
471E92350.09
472Q92350.09
481E106260.05
482A106260.05
491E104070.07
492D104070.07
501E105350.06
502H105350.06
511E102590.07
512I102590.07
521G92920.08
522Q92920.08
531G103790.06
532A103790.06
541G105320.04
542D105320.04
551G104330.06
552H104330.06
561G103360.05
562I103360.05
571Q91980.08
572A91980.08
581Q92820.08
582D92820.08
591Q92670.09
592H92670.09
601Q93080.07
602I93080.07
611A103870.06
612D103870.06
621A104920.06
622H104920.06
631A102180.06
632I102180.06
641D104780.06
642H104780.06
651D103450.05
652I103450.05
661H102890.06
662I102890.06
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 696 -
Rwork0.307 13229 -
obs--99.89 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.87470.08880.3020.04370.10820.34220.06820.0879-0.01130.0226-0.0351-0.00180.03560.0128-0.03310.0223-0.02980.00520.265-0.01370.2642-107.9438-37.8934479.5777
20.5190.1928-0.0780.64450.33170.279-0.01680.0215-0.0282-0.10480.1419-0.0674-0.05390.0577-0.12510.0287-0.07310.0220.2612-0.0760.2841-55.5306-14.8138500.6158
30.1955-0.2924-0.22820.77220.45870.5229-0.09380.0763-0.0330.1289-0.00110.08510.05790.01430.09490.0537-0.04470.02070.2478-0.02420.2732-108.5011-4.4307528.2333
40.32110.17220.1070.73270.40130.3715-0.108-0.0420.0337-0.12910.03930.0961-0.04310.03150.06870.05050.0112-0.02570.23130.01410.2631-60.7525-91.7023453.2128
51.79440.1127-0.93671.08340.77491.82250.05240.07990.07550.08910.1065-0.006-0.3688-0.2407-0.15880.25470.13780.05110.40520.1590.066-106.8723-18.4447565.9233
60.7508-0.3902-0.35810.20420.19660.26820.07190.08120.0741-0.0325-0.0504-0.02970.0168-0.0767-0.02150.03920.0276-0.00270.3208-0.00470.2271-60.5676-42.5406461.1179
70.6738-0.04430.22750.3101-0.040.2230.06150.01690.0613-0.0243-0.0296-0.1498-0.0074-0.0738-0.03180.0312-0.0050.00760.2354-0.00470.2694-7.3452-65.3843440.3377
80.7070.10131.14030.1551-0.03072.27520.1636-0.1473-0.1557-0.07360.0777-0.08250.4645-0.2627-0.24120.1339-0.0876-0.03630.36470.05270.1585-59.09-78.2608414.7716
90.66280.41370.32810.26670.22320.2140.0719-0.0513-0.08180.035-0.0402-0.02750.0045-0.0383-0.03170.0299-0.02990.00040.29440.01540.2597-108.2993-54.253520.8785
100.7410.0648-0.29470.38390.12820.31150.1066-0.0241-0.03340.0777-0.0187-0.14760.0196-0.0614-0.08790.0687-0.0133-0.0590.20280.01310.2467-54.9317-30.7217541.0139
110.6953-0.0358-0.26260.03220.08380.32380.068-0.04750.0369-0.0084-0.02650.0025-0.0035-0.0025-0.04150.02840.0113-0.00090.2672-0.00220.2723-60.1488-59.0878502.2997
120.6254-0.21060.11480.57260.30850.4286-0.0274-0.00810.07180.13320.1701-0.07450.0950.0583-0.14270.0420.0757-0.04270.2466-0.07520.2901-7.9612-81.8046480.5974
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 327
2X-RAY DIFFRACTION2C1 - 327
3X-RAY DIFFRACTION3F1 - 327
4X-RAY DIFFRACTION4O1 - 327
5X-RAY DIFFRACTION5P1 - 327
6X-RAY DIFFRACTION6E1 - 327
7X-RAY DIFFRACTION7G1 - 327
8X-RAY DIFFRACTION8Q1 - 327
9X-RAY DIFFRACTION9A1 - 327
10X-RAY DIFFRACTION10D1 - 327
11X-RAY DIFFRACTION11H1 - 327
12X-RAY DIFFRACTION12I1 - 327

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more