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- PDB-6h4m: TarP-UDP-GlcNAc-3RboP -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6h4m
TitleTarP-UDP-GlcNAc-3RboP
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 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / URIDINE-5'-DIPHOSPHATE / Poly(ribitol-phosphate) beta-N-acetylglucosaminyltransferase TarP
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.73 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
DepositionJul 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)494,46363
Polymers478,66412
Non-polymers15,79951
Water18,7001038
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)123,70817
Polymers119,6663
Non-polymers4,04214
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-122 kcal/mol
Surface area37380 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)123,70817
Polymers119,6663
Non-polymers4,04214
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-124 kcal/mol
Surface area37580 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)123,47016
Polymers119,6663
Non-polymers3,80313
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-105 kcal/mol
Surface area38410 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)123,57813
Polymers119,6663
Non-polymers3,91110
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-81 kcal/mol
Surface area38050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.170, 210.750, 123.200
Angle α, β, γ (deg.)90.00, 91.92, 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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010B1 - 327
2010C1 - 327
1020B1 - 327
2020F1 - 327
1030B1 - 327
2030O1 - 327
1040B1 - 327
2040P1 - 327
1050B1 - 327
2050E1 - 327
1060B1 - 327
2060G1 - 327
1070B1 - 327
2070Q1 - 327
1080B1 - 327
2080A1 - 327
1090B1 - 327
2090D1 - 327
10100B1 - 327
20100H1 - 327
10110B1 - 327
20110I1 - 327
10120C1 - 327
20120F1 - 327
10130C1 - 327
20130O1 - 327
10140C1 - 326
20140P1 - 326
10150C1 - 327
20150E1 - 327
10160C1 - 327
20160G1 - 327
10170C1 - 327
20170Q1 - 327
10180C1 - 327
20180A1 - 327
10190C1 - 327
20190D1 - 327
10200C1 - 327
20200H1 - 327
10210C1 - 327
20210I1 - 327
10220F1 - 327
20220O1 - 327
10230F1 - 326
20230P1 - 326
10240F1 - 326
20240E1 - 326
10250F1 - 327
20250G1 - 327
10260F1 - 327
20260Q1 - 327
10270F1 - 327
20270A1 - 327
10280F1 - 327
20280D1 - 327
10290F1 - 327
20290H1 - 327
10300F1 - 327
20300I1 - 327
10310O1 - 326
20310P1 - 326
10320O1 - 326
20320E1 - 326
10330O1 - 327
20330G1 - 327
10340O1 - 327
20340Q1 - 327
10350O1 - 327
20350A1 - 327
10360O1 - 327
20360D1 - 327
10370O1 - 327
20370H1 - 327
10380O1 - 327
20380I1 - 327
10390P1 - 327
20390E1 - 327
10400P1 - 326
20400G1 - 326
10410P1 - 327
20410Q1 - 327
10420P1 - 327
20420A1 - 327
10430P1 - 326
20430D1 - 326
10440P1 - 326
20440H1 - 326
10450P1 - 327
20450I1 - 327
10460E1 - 327
20460G1 - 327
10470E1 - 327
20470Q1 - 327
10480E1 - 327
20480A1 - 327
10490E1 - 327
20490D1 - 327
10500E1 - 327
20500H1 - 327
10510E1 - 327
20510I1 - 327
10520G1 - 327
20520Q1 - 327
10530G1 - 327
20530A1 - 327
10540G1 - 327
20540D1 - 327
10550G1 - 327
20550H1 - 327
10560G1 - 327
20560I1 - 327
10570Q1 - 327
20570A1 - 327
10580Q1 - 327
20580D1 - 327
10590Q1 - 327
20590H1 - 327
10600Q1 - 327
20600I1 - 327
10610A1 - 327
20610D1 - 327
10620A1 - 327
20620H1 - 327
10630A1 - 327
20630I1 - 327
10640D1 - 327
20640H1 - 327
10650D1 - 327
20650I1 - 327
10660H1 - 327
20660I1 - 327

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

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Components

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Protein , 1 types, 12 molecules BCFOPEGQADHI

#1: Protein
Probable ss-1,3-N-acetylglucosaminyltransferase


Mass: 39888.680 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Gene: SA1808 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JNB0

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Non-polymers , 6 types, 1089 molecules

#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
#3: Chemical
ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1038 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 25% PEG 3350, 250 mM magnesium chloride, 0.1 M sodium citrate, pH 5.7.
PH range: 5.4-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.73→48.4 Å / Num. obs: 128233 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 8.4
Reflection shellResolution: 2.73→2.8 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.73→48.44 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 28.851 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23323 6412 5 %RANDOM
Rwork0.18852 ---
obs0.19077 121821 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.563 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å2-0.23 Å2
2--0.96 Å20 Å2
3---0.23 Å2
Refinement stepCycle: 1 / Resolution: 2.73→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28906 0 961 1038 30905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01430336
X-RAY DIFFRACTIONr_bond_other_d0.0020.01726307
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.69541130
X-RAY DIFFRACTIONr_angle_other_deg0.9671.67661170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31953745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00123.8881371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.456154965
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9721599
X-RAY DIFFRACTIONr_chiral_restr0.0510.24330
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0233369
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025702
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_it5.27210.89515067
X-RAY DIFFRACTIONr_mcbond_other5.26810.89515066
X-RAY DIFFRACTIONr_mcangle_it7.45614.70218781
X-RAY DIFFRACTIONr_mcangle_other7.45614.70218782
X-RAY DIFFRACTIONr_scbond_it7.43812.08315269
X-RAY DIFFRACTIONr_scbond_other7.43812.08315268
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.9315.98522350
X-RAY DIFFRACTIONr_long_range_B_refined11.48262.505128781
X-RAY DIFFRACTIONr_long_range_B_other11.48562.46128508
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)
11B103850.06
12C103850.06
21B104240.06
22F104240.06
31B105580.06
32O105580.06
41B86680.06
42P86680.06
51B105010.07
52E105010.07
61B103970.06
62G103970.06
71B90220.08
72Q90220.08
81B105370.06
82A105370.06
91B103370.06
92D103370.06
101B107130.06
102H107130.06
111B103130.07
112I103130.07
121C103650.06
122F103650.06
131C104320.05
132O104320.05
141C86650.06
142P86650.06
151C102740.07
152E102740.07
161C103880.06
162G103880.06
171C90750.07
172Q90750.07
181C103010.06
182A103010.06
191C102770.06
192D102770.06
201C103850.07
202H103850.07
211C103580.06
212I103580.06
221F105050.06
222O105050.06
231F86550.05
232P86550.05
241F103070.06
242E103070.06
251F103410.06
252G103410.06
261F90710.07
262Q90710.07
271F103960.06
272A103960.06
281F102690.05
282D102690.05
291F103850.07
292H103850.07
301F103110.06
302I103110.06
311O86840.06
312P86840.06
321O103600.07
322E103600.07
331O103780.06
332G103780.06
341O90450.07
342Q90450.07
351O104550.06
352A104550.06
361O103330.05
362D103330.05
371O105270.07
372H105270.07
381O103690.06
382I103690.06
391P85690.06
392E85690.06
401P86540.06
402G86540.06
411P83160.07
412Q83160.07
421P86030.06
422A86030.06
431P85870.06
432D85870.06
441P85910.07
442H85910.07
451P87020.05
452I87020.05
461E102060.07
462G102060.07
471E89440.08
472Q89440.08
481E105820.06
482A105820.06
491E102270.06
492D102270.06
501E104770.07
502H104770.07
511E102200.07
512I102200.07
521G90420.07
522Q90420.07
531G102460.06
532A102460.06
541G103040.05
542D103040.05
551G103340.07
552H103340.07
561G102700.06
562I102700.06
571Q90530.07
572A90530.07
581Q89290.06
582D89290.06
591Q90840.07
592H90840.07
601Q90980.07
602I90980.07
611A102420.06
612D102420.06
621A106080.06
622H106080.06
631A102680.06
632I102680.06
641D103200.07
642H103200.07
651D101550.05
652I101550.05
661H103180.07
662I103180.07
LS refinement shellResolution: 2.73→2.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 473 -
Rwork0.326 8984 -
obs--99.79 %
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)
10.9373-0.10850.41170.0574-0.15020.42930.0535-0.069-0.0123-0.0244-0.02520.0070.04910.0036-0.02840.08060.01290.08430.28350.00420.1374-1.088755.625210.9259
20.596-0.0847-0.0890.3475-0.18460.21570.01030.0021-0.03660.04980.07770.0576-0.03950.0103-0.0880.1030.04720.10530.25340.0430.1513-53.251678.566-10.2332
30.16640.1902-0.14670.5757-0.36090.6045-0.1133-0.0766-0.046-0.113-0.0127-0.06990.04040.0030.1260.11480.03560.07790.25920.02590.149-0.64888.718-37.6663
40.2262-0.11810.10870.5353-0.37810.4551-0.10730.0540.02580.12660.0066-0.0724-0.0605-0.01580.10070.1136-0.02270.05080.2665-0.01430.1121-48.41411.724337.1732
50.2438-0.0541-0.5290.02360.10161.3850.1012-0.07950.0008-0.02340.07260.0021-0.44110.1313-0.17380.2523-0.08430.16090.3842-0.02750.1258-2.233575.1936-75.8838
60.75130.3205-0.46080.1513-0.23090.36480.0679-0.04740.07840.0141-0.03130.03180.00140.0403-0.03660.0838-0.02450.07880.3563-0.00430.0908-48.417950.740129.4127
70.73310.23530.30740.507-0.00210.22410.089-0.03750.0976-0.0039-0.10780.18530.01660.0820.01890.10190.02980.05780.2637-0.04230.1468-101.436528.279950.1178
80.4646-0.05630.88440.4706-0.08931.69740.17110.1595-0.12590.0050.08490.08570.31030.2701-0.2560.1480.1295-0.00880.3839-0.06250.0776-50.540515.333276.0183
90.7502-0.21370.30280.1743-0.21530.27530.06080.0181-0.0952-0.0205-0.02960.00540.00690.0109-0.03120.08820.03560.07680.324-0.03660.118-0.746639.0506-30.5717
100.7011-0.18310.00250.4829-0.07160.25280.13690.059-0.0851-0.0398-0.13030.1753-0.03250.0942-0.00650.12660.02160.05240.2431-0.04720.1233-54.007462.5575-50.653
110.52230.1039-0.21570.0969-0.18020.36460.07270.02180.00870.0159-0.02590.0183-0.01970.0286-0.04680.0749-0.00110.0810.3091-0.00740.135-48.641834.1819-11.9602
120.85350.29160.22030.6672-0.12520.1356-0.05840.01380.0233-0.14770.09970.0820.0221-0.0021-0.04130.1055-0.06660.03740.27690.04260.1511-100.835611.64379.7749
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

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