[English] 日本語
Yorodumi
- PDB-5n5v: Structure of p-boronophenylalanyl tRNA synthetase - apo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n5v
TitleStructure of p-boronophenylalanyl tRNA synthetase - apo form
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / aminoacylation / non-natural amino acid / synthetic biology
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, type 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs ...Tyrosine-tRNA ligase, type 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSchiefner, A. / Skerra, A.
CitationJournal: Biochemistry / Year: 2018
Title: Structural Basis for the Specific Cotranslational Incorporation of p-Boronophenylalanine into Biosynthetic Proteins.
Authors: Schiefner, A. / Nastle, L. / Landgraf, M. / Reichert, A.J. / Skerra, A.
History
DepositionFeb 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
A: Tyrosine--tRNA ligase
B: Tyrosine--tRNA ligase
C: Tyrosine--tRNA ligase
D: Tyrosine--tRNA ligase
E: Tyrosine--tRNA ligase
F: Tyrosine--tRNA ligase
G: Tyrosine--tRNA ligase
H: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,99113
Polymers287,8148
Non-polymers1775
Water3,549197
1
A: Tyrosine--tRNA ligase
B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0244
Polymers71,9532
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-50 kcal/mol
Surface area27980 Å2
MethodPISA
2
C: Tyrosine--tRNA ligase
D: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9893
Polymers71,9532
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-42 kcal/mol
Surface area28060 Å2
MethodPISA
3
E: Tyrosine--tRNA ligase
F: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9893
Polymers71,9532
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-40 kcal/mol
Surface area28100 Å2
MethodPISA
4
G: Tyrosine--tRNA ligase
H: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9893
Polymers71,9532
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-40 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.001, 94.008, 286.566
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA1 - 3061 - 306
21LEULEUBB1 - 3061 - 306
12ARGARGAA1 - 3051 - 305
22ARGARGCC1 - 3051 - 305
13HISHISAA1 - 3091 - 309
23HISHISDD1 - 3091 - 309
14HISHISAA1 - 3091 - 309
24HISHISEE1 - 3091 - 309
15HISHISAA1 - 3091 - 309
25HISHISFF1 - 3091 - 309
16HISHISAA1 - 3091 - 309
26HISHISGG1 - 3091 - 309
17LEULEUAA1 - 3061 - 306
27LEULEUHH1 - 3061 - 306
18ARGARGBB1 - 3051 - 305
28ARGARGCC1 - 3051 - 305
19LEULEUBB1 - 3061 - 306
29LEULEUDD1 - 3061 - 306
110LEULEUBB1 - 3061 - 306
210LEULEUEE1 - 3061 - 306
111LEULEUBB1 - 3061 - 306
211LEULEUFF1 - 3061 - 306
112LEULEUBB1 - 3061 - 306
212LEULEUGG1 - 3061 - 306
113SERSERBB1 - 3071 - 307
213SERSERHH1 - 3071 - 307
114ARGARGCC1 - 3051 - 305
214ARGARGDD1 - 3051 - 305
115ARGARGCC1 - 3051 - 305
215ARGARGEE1 - 3051 - 305
116ARGARGCC1 - 3051 - 305
216ARGARGFF1 - 3051 - 305
117ARGARGCC1 - 3051 - 305
217ARGARGGG1 - 3051 - 305
118ARGARGCC1 - 3051 - 305
218ARGARGHH1 - 3051 - 305
119HISHISDD1 - 3091 - 309
219HISHISEE1 - 3091 - 309
120HISHISDD1 - 3091 - 309
220HISHISFF1 - 3091 - 309
121HISHISDD1 - 3091 - 309
221HISHISGG1 - 3091 - 309
122LEULEUDD1 - 3061 - 306
222LEULEUHH1 - 3061 - 306
123HISHISEE1 - 3091 - 309
223HISHISFF1 - 3091 - 309
124HISHISEE1 - 3091 - 309
224HISHISGG1 - 3091 - 309
125LEULEUEE1 - 3061 - 306
225LEULEUHH1 - 3061 - 306
126HISHISFF1 - 3091 - 309
226HISHISGG1 - 3091 - 309
127LEULEUFF1 - 3061 - 306
227LEULEUHH1 - 3061 - 306
128LEULEUGG1 - 3061 - 306
228LEULEUHH1 - 3061 - 306

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

-
Components

#1: Protein
Tyrosine--tRNA ligase / Tyrosyl-tRNA synthetase / TyrRS


Mass: 35976.734 Da / Num. of mol.: 8 / Mutation: M6L, Y32S, L65A, H70M, D158S, L162E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Gene: tyrS, MJ0389 / Plasmid: pASK75-BpaRS-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 16 % (w/v) PEG 4000, 0.2 M MgCl2, 0.1 M Tris/HCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8943 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2016
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8943 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.505
11h,-k,-l20.495
ReflectionResolution: 2.3→34.91 Å / Num. obs: 124992 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.808 % / Biso Wilson estimate: 34.372 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.196 / Rrim(I) all: 0.213 / Χ2: 0.937 / Net I/σ(I): 8.99 / Num. measured all: 850976 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.46.8650.9352.03148850.6021.012100
2.4-2.56.8720.7992.35125770.6910.865100
2.5-2.66.8820.6592.92107590.7370.714100
2.6-2.86.8590.5023.82172220.8450.544100
2.8-36.8970.3525.49128870.9030.382100
3-3.56.8510.2049.34208890.9690.221100
3.5-46.7250.11216.41117220.9890.122100
4-66.6970.08420.03168680.9940.092100
6-86.6920.0819.8241250.9960.087100
8-106.3640.05227.6914820.9980.05799.8
10-34.915.9610.04730.5515760.9980.05197

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5n5u
Resolution: 2.3→34.91 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.887 / SU B: 9.545 / SU ML: 0.122 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 6047 4.8 %RANDOM
Rwork0.2123 ---
obs0.2138 118944 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.09 Å2 / Biso mean: 33.229 Å2 / Biso min: 2.51 Å2
Baniso -1Baniso -2Baniso -3
1--28.78 Å2-0 Å2-0.69 Å2
2---2.36 Å20 Å2
3---31.14 Å2
Refinement stepCycle: final / Resolution: 2.3→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19733 0 5 197 19935
Biso mean--28.19 16.99 -
Num. residues----2465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01920050
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220141
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.99426894
X-RAY DIFFRACTIONr_angle_other_deg0.983346607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07152457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21124.748893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12154052
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.78115120
X-RAY DIFFRACTIONr_chiral_restr0.0920.22985
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221997
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024133
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A193060.07
12B193060.07
21A193560.05
22C193560.05
31A195300.06
32D195300.06
41A196100.05
42E196100.05
51A195420.05
52F195420.05
61A196720.05
62G196720.05
71A194320.05
72H194320.05
81B193300.05
82C193300.05
91B196040.05
92D196040.05
101B194420.06
102E194420.06
111B195420.05
112F195420.05
121B194780.06
122G194780.06
131B196400.06
132H196400.06
141C193480.05
142D193480.05
151C195220.04
152E195220.04
161C193740.05
162F193740.05
171C194680.05
172G194680.05
181C193500.05
182H193500.05
191D196440.05
192E196440.05
201D198100.04
202F198100.04
211D195620.06
212G195620.06
221D196860.04
222H196860.04
231E196940.05
232F196940.05
241E196660.05
242G196660.05
251E193580.06
252H193580.06
261F195500.06
262G195500.06
271F196100.03
272H196100.03
281G194760.06
282H194760.06
LS refinement shellResolution: 2.299→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 473 -
Rwork0.253 8500 -
all-8973 -
obs--98.89 %
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)
13.0019-0.2393-0.69441.77450.62290.70140.01780.15670.0136-0.0686-0.10860.04660.07030.08480.09080.1610.0014-0.02140.09820.0280.087935.0445-183.9212271.1461
20.29710.4656-0.59591.1213-0.7711.29040.0183-0.0643-0.00740.1082-0.0042-0.17160.01640.1939-0.01410.16210.0088-0.02520.1234-0.01660.117929.5215-189.5904281.1042
32.41150.02630.13593.18051.15571.7657-0.02650.1738-0.0847-0.190.1143-0.14430.0890.0147-0.08780.17270.0002-0.00610.05610.01650.031956.2503-193.0434264.3173
41.97870.7446-1.33391.4015-0.261.01090.0821-0.09330.18730.014-0.03040.1221-0.13110.0272-0.05170.19390.0109-0.05860.1213-0.04190.088112.0215-197.0288309.0947
50.734-0.4275-0.14870.3891-0.47415.54170.0524-0.0195-0.0143-0.1101-0.0450.0287-0.1304-0.5552-0.00740.14290.0945-0.0450.2031-0.01190.045417.1059-199.4456298.4391
62.87850.53340.0330.97340.08670.25340.0253-0.03050.15420.0706-0.01050.12020.01930.0117-0.01480.19290.0075-0.0340.0574-0.00620.0294-4.7696-209.7594312.894
72.1020.0673-0.16991.3745-0.12852.7230.04780.14630.1602-0.034-0.01120.075-0.0651-0.2507-0.03660.18420.02290.00910.03290.01250.016215.1871-170.8373381.8091
80.7002-1.0932-0.51721.74691.04032.54550.0053-0.06-0.107-0.04260.04620.14750.19660.0081-0.05150.23860.02250.00030.12830.02840.02626.4496-182.2958380.1528
93.2760.09750.04731.654-0.0172.4409-0.0154-0.15420.13610.12620.02830.1356-0.0064-0.0477-0.01290.2364-0.04630.01490.19780.01520.051-4.6586-176.9386395.8459
102.2687-0.8161-0.48541.29530.05390.120.0249-0.00490.07830.0272-0.0212-0.1365-0.02910.0058-0.00370.243-0.02220.00110.0604-0.00290.014942.0388-197.1168355.8532
117.9796-1.37040.06050.8161-0.08560.01170.1125-0.51680.23710.1259-0.1401-0.3392-0.01190.04440.02770.4060.0148-0.02680.3628-0.04060.268769.5506-217.0531344.8609
122.4087-0.24380.08313.3686-0.65541.98340.05360.229-0.07390.0091-0.0367-0.14820.19710.2133-0.0170.26340.05230.00640.1678-0.03580.04162.6376-209.1384348.9038
131.47090.581.07861.26020.21131.95020.0637-0.10240.07090.09780.03710.0785-0.0107-0.1348-0.10080.21110.01220.02050.04560.0160.0284-6.6251-168.2851335.9596
144.29830.1373-1.19872.9165-0.47971.2366-0.00840.01430.1249-0.1097-0.06090.0735-0.230.15640.06930.20350.0445-0.01010.18030.02760.0374-29.5395-164.318324.369
153.2602-0.38740.62490.41920.57032.70330.14140.1568-0.1032-0.1717-0.1460.11610.14010.11780.00460.36760.0517-0.00820.2279-0.03620.1339-33.2699-170.1992318.9366
163.5375.20672.210311.77342.22911.6430.0089-0.0973-0.18530.35560.0313-0.5934-0.0834-0.0561-0.04030.2880.02260.0520.386-0.02020.148314.426-135.6071379.4482
171.64930.81031.10032.15020.48791.43180.06810.0057-0.0322-0.0916-0.0728-0.09050.01310.12080.00470.20180.00540.02130.02520.00670.006811.3178-149.3541361.4328
183.23320.0345-0.75462.3438-0.42761.59720.1017-0.14750.07880.09560.0011-0.0244-0.10410.0242-0.10280.2593-0.0324-0.00050.0994-0.00240.080535.7647-135.1517364.9237
191.0759-0.19130.77540.0598-0.12920.56350.03160.0483-0.0405-0.0566-0.01380.00280.00640.0336-0.01780.24810.01290.04430.1279-0.00150.0729.4027-154.4436440.8449
207.9444.1395-0.26777.2899-1.75990.52140.4693-0.50650.136-0.0331-0.45920.03510.07210.0715-0.01010.3265-0.00890.06450.2087-0.0230.114233.4734-154.6873462.1891
211.8013-0.2407-0.56744.07111.13590.81010.1157-0.2369-0.05430.1398-0.1008-0.1379-0.2521-0.1589-0.01490.26980.0748-0.01060.18180.0060.007131.6583-153.0054455.8875
223.8702-0.71840.41192.64890.59810.2260.11850.125-0.1719-0.0193-0.0618-0.08160.00990.0141-0.05670.1644-0.0118-0.01280.0982-0.0590.0469-17.2569-145.1608403.7578
230.9916-0.7841.05621.3319-0.06543.01530.06880.1031-0.03430.0381-0.14570.2391-0.06-0.09810.07690.11770.00960.0480.043-0.00620.0771-10.062-145.6083413.3415
242.46230.2979-0.11413.2080.30191.74090.0210.0811-0.1071-0.0546-0.03570.1338-0.02020.09240.01460.12790.01090.02080.0639-0.02180.022-37.472-132.7358402.7421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 79
2X-RAY DIFFRACTION2A80 - 196
3X-RAY DIFFRACTION3A197 - 309
4X-RAY DIFFRACTION4B1 - 136
5X-RAY DIFFRACTION5B137 - 167
6X-RAY DIFFRACTION6B168 - 307
7X-RAY DIFFRACTION7C1 - 111
8X-RAY DIFFRACTION8C112 - 195
9X-RAY DIFFRACTION9C196 - 306
10X-RAY DIFFRACTION10D1 - 249
11X-RAY DIFFRACTION11D250 - 264
12X-RAY DIFFRACTION12D265 - 309
13X-RAY DIFFRACTION13E1 - 195
14X-RAY DIFFRACTION14E196 - 257
15X-RAY DIFFRACTION15E258 - 309
16X-RAY DIFFRACTION16F1 - 6
17X-RAY DIFFRACTION17F7 - 196
18X-RAY DIFFRACTION18F197 - 309
19X-RAY DIFFRACTION19G1 - 250
20X-RAY DIFFRACTION20G251 - 257
21X-RAY DIFFRACTION21G258 - 309
22X-RAY DIFFRACTION22H1 - 85
23X-RAY DIFFRACTION23H86 - 195
24X-RAY DIFFRACTION24H196 - 307

+
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://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