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- PDB-5uk3: Crystal structure of cyanase from T. urticae -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5uk3
TitleCrystal structure of cyanase from T. urticae
ComponentsUncharacterized protein
KeywordsLYASE / Tetranychus urticae / cyanase / agricultural pest / two-spotted spidermite / spider mite
Function / homology
Function and homology information


cyanate metabolic process / cyanate hydratase activity / DNA binding
Similarity search - Function
Cyanate lyase, C-terminal / Cyanate hydratase / Cyanate lyase, C-terminal domain superfamily / Cyanate lyase C-terminal domain / Cyanate lyase C-terminal domain, Cyanate hydratase / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Cyanate_lyase domain-containing protein
Similarity search - Component
Biological speciesTetranychus urticae (two-spotted spider mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSchlachter, C.R. / Chruszcz, M.
CitationJournal: J. Agric. Food Chem. / Year: 2017
Title: Structural Characterization of a Eukaryotic Cyanase from Tetranychus urticae.
Authors: Schlachter, C.R. / Klapper, V. / Wybouw, N. / Radford, T. / Van Leeuwen, T. / Grbic, M. / Chruszcz, M.
History
DepositionJan 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
I: Uncharacterized protein
J: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)202,41110
Polymers202,41110
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50730 Å2
ΔGint-269 kcal/mol
Surface area53410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.074, 81.611, 136.466
Angle α, β, γ (deg.)90.00, 100.37, 90.00
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
18A
28I
19A
29J
110B
210C
111B
211D
112B
212E
113B
213F
114B
214G
115B
215H
116B
216I
117B
217J
118C
218D
119C
219E
120C
220F
121C
221G
122C
222H
123C
223I
124C
224J
125D
225E
126D
226F
127D
227G
128D
228H
129D
229I
130D
230J
131E
231F
132E
232G
133E
233H
134E
234I
135E
235J
136F
236G
137F
237H
138F
238I
139F
239J
140G
240H
141G
241I
142G
242J
143H
243I
144H
244J
145I
245J

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA22 - 15522 - 155
21LYSLYSBB22 - 15522 - 155
12LYSLYSAA22 - 15522 - 155
22LYSLYSCC22 - 15522 - 155
13LYSLYSAA22 - 15522 - 155
23LYSLYSDD22 - 15522 - 155
14LYSLYSAA22 - 15522 - 155
24LYSLYSEE22 - 15522 - 155
15LYSLYSAA22 - 15522 - 155
25LYSLYSFF22 - 15522 - 155
16LYSLYSAA22 - 15522 - 155
26LYSLYSGG22 - 15522 - 155
17LYSLYSAA22 - 15522 - 155
27LYSLYSHH22 - 15522 - 155
18LYSLYSAA22 - 15522 - 155
28LYSLYSII22 - 15522 - 155
19LYSLYSAA22 - 15522 - 155
29LYSLYSJJ22 - 15522 - 155
110GLNGLNBB22 - 15722 - 157
210GLNGLNCC22 - 15722 - 157
111GLNGLNBB22 - 15722 - 157
211GLNGLNDD22 - 15722 - 157
112LEULEUBB22 - 15822 - 158
212LEULEUEE22 - 15822 - 158
113GLNGLNBB22 - 15722 - 157
213GLNGLNFF22 - 15722 - 157
114GLNGLNBB22 - 15722 - 157
214GLNGLNGG22 - 15722 - 157
115GLNGLNBB22 - 15722 - 157
215GLNGLNHH22 - 15722 - 157
116GLNGLNBB22 - 15722 - 157
216GLNGLNII22 - 15722 - 157
117GLNGLNBB22 - 15722 - 157
217GLNGLNJJ22 - 15722 - 157
118ASPASPCC22 - 15922 - 159
218ASPASPDD22 - 15922 - 159
119GLNGLNCC22 - 15722 - 157
219GLNGLNEE22 - 15722 - 157
120ASPASPCC22 - 15922 - 159
220ASPASPFF22 - 15922 - 159
121ASPASPCC22 - 15922 - 159
221ASPASPGG22 - 15922 - 159
122GLNGLNCC22 - 15722 - 157
222GLNGLNHH22 - 15722 - 157
123LEULEUCC22 - 15822 - 158
223LEULEUII22 - 15822 - 158
124ASPASPCC22 - 15922 - 159
224ASPASPJJ22 - 15922 - 159
125GLNGLNDD22 - 15722 - 157
225GLNGLNEE22 - 15722 - 157
126ASPASPDD22 - 15922 - 159
226ASPASPFF22 - 15922 - 159
127ASPASPDD22 - 15922 - 159
227ASPASPGG22 - 15922 - 159
128GLNGLNDD22 - 15722 - 157
228GLNGLNHH22 - 15722 - 157
129LEULEUDD22 - 15822 - 158
229LEULEUII22 - 15822 - 158
130ASPASPDD22 - 15922 - 159
230ASPASPJJ22 - 15922 - 159
131GLNGLNEE22 - 15722 - 157
231GLNGLNFF22 - 15722 - 157
132GLNGLNEE22 - 15722 - 157
232GLNGLNGG22 - 15722 - 157
133GLNGLNEE22 - 15722 - 157
233GLNGLNHH22 - 15722 - 157
134GLNGLNEE22 - 15722 - 157
234GLNGLNII22 - 15722 - 157
135GLNGLNEE22 - 15722 - 157
235GLNGLNJJ22 - 15722 - 157
136ASPASPFF22 - 15922 - 159
236ASPASPGG22 - 15922 - 159
137GLNGLNFF22 - 15722 - 157
237GLNGLNHH22 - 15722 - 157
138LEULEUFF22 - 15822 - 158
238LEULEUII22 - 15822 - 158
139ASPASPFF22 - 15922 - 159
239ASPASPJJ22 - 15922 - 159
140GLNGLNGG22 - 15722 - 157
240GLNGLNHH22 - 15722 - 157
141LEULEUGG22 - 15822 - 158
241LEULEUII22 - 15822 - 158
142ASPASPGG22 - 15922 - 159
242ASPASPJJ22 - 15922 - 159
143GLNGLNHH22 - 15722 - 157
243GLNGLNII22 - 15722 - 157
144GLNGLNHH22 - 15722 - 157
244GLNGLNJJ22 - 15722 - 157
145LEULEUII22 - 15822 - 158
245LEULEUJJ22 - 15822 - 158

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

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Components

#1: Protein
Uncharacterized protein / cyanase


Mass: 20241.080 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite)
Plasmid: pMBPcs1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: T1KZQ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 7.5, 15% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 38010 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.05 / Rrim(I) all: 0.102 / Rsym value: 0.069 / Net I/σ(I): 22.5
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2 / Num. unique obs: 1906 / CC1/2: 0.8 / Rpim(I) all: 0.35 / Rrim(I) all: 0.721 / Rsym value: 0.546 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IV1
Resolution: 2.8→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 42.766 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23997 1886 5 %RANDOM
Rwork0.2206 ---
obs0.22159 36100 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 93.263 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å27.24 Å2
2---4.51 Å20 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10776 0 0 20 10796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910983
X-RAY DIFFRACTIONr_bond_other_d00.0210558
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.95414845
X-RAY DIFFRACTIONr_angle_other_deg3.684324151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95951372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81624.464504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39151931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3131560
X-RAY DIFFRACTIONr_chiral_restr0.0930.21684
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212568
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022614
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_it3.2125.8875512
X-RAY DIFFRACTIONr_mcbond_other3.2125.8875511
X-RAY DIFFRACTIONr_mcangle_it5.2148.8256876
X-RAY DIFFRACTIONr_mcangle_other5.2148.8256877
X-RAY DIFFRACTIONr_scbond_it3.5286.1775471
X-RAY DIFFRACTIONr_scbond_other3.5286.1775469
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8879.1357969
X-RAY DIFFRACTIONr_long_range_B_refined8.65546.2212245
X-RAY DIFFRACTIONr_long_range_B_other8.65546.2112241
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)
11A136200.12
12B136200.12
21A138540.12
22C138540.12
31A139320.12
32D139320.12
41A138880.11
42E138880.11
51A137340.12
52F137340.12
61A137900.11
62G137900.11
71A136380.12
72H136380.12
81A135520.12
82I135520.12
91A136000.12
92J136000.12
101B144020.1
102C144020.1
111B144220.1
112D144220.1
121B143460.1
122E143460.1
131B139880.11
132F139880.11
141B138420.1
142G138420.1
151B141580.11
152H141580.11
161B140560.11
162I140560.11
171B140960.11
172J140960.11
181C146180.11
182D146180.11
191C143320.12
192E143320.12
201C143000.11
202F143000.11
211C140660.12
212G140660.12
221C142960.1
222H142960.1
231C142900.11
232I142900.11
241C143460.12
242J143460.12
251D145580.11
252E145580.11
261D142700.11
262F142700.11
271D141820.11
272G141820.11
281D142720.11
282H142720.11
291D144280.11
292I144280.11
301D145180.11
302J145180.11
311E142540.11
312F142540.11
321E142080.08
322G142080.08
331E141520.11
332H141520.11
341E142060.11
342I142060.11
351E143160.12
352J143160.12
361F141000.1
362G141000.1
371F141360.12
372H141360.12
381F138840.11
382I138840.11
391F141120.11
392J141120.11
401G140160.12
402H140160.12
411G140720.1
412I140720.1
421G141640.12
422J141640.12
431H140880.11
432I140880.11
441H141860.13
442J141860.13
451I142420.11
452J142420.11
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 145 -
Rwork0.341 2556 -
obs--97.26 %
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)
18.249-1.94963.78792.1028-2.4453.5620.2638-0.7782-0.14740.2615-0.00430.4512-0.1177-0.5288-0.25950.3614-0.09890.41240.4296-0.19910.579627.384341.410349.216
22.2329-1.47490.41392.8350.26941.52120.1786-0.20440.05450.6886-0.0990.3548-0.0687-0.1296-0.07960.4996-0.12850.14210.2217-0.10940.310245.954137.200243.5755
31.99681.04020.9862.56020.261.6190.2638-0.14610.25120.2927-0.22530.9906-0.1578-0.4608-0.03850.15190.06840.03240.44510.00760.580226.471928.182618.2204
44.15172.26970.48163.68480.74590.54790.21440.10580.32490.0013-0.07350.2974-0.2252-0.1447-0.14090.24170.0684-0.01230.15890.0990.336144.276134.776712.0085
55.31420.9444-1.65673.8794-0.00852.47050.17680.0493-0.01430.2396-0.11970.27460.0676-0.3614-0.05710.1203-0.0441-0.18220.4335-0.08170.451221.8454-0.579816.4187
62.30121.0087-0.8122.8151-2.07292.9916-0.02930.1677-0.2368-0.23230.03410.26090.0722-0.2558-0.00480.13510.0031-0.16740.3311-0.10230.262345.6712-0.134911.9999
76.2251.4578-1.15742.3714-1.25174.43710.3115-0.1178-0.09460.6246-0.06880.9018-0.4761-0.3276-0.24270.1830.00240.21420.27120.03290.510929.5575-13.05944.7974
82.6147-0.3287-3.16312.03151.995.1831-0.0662-0.3174-0.1880.3426-0.1590.12440.31940.2970.22520.2130.0026-0.08850.2437-0.01030.268152.9975-10.841539.8714
95.5586-1.0028-1.69285.44381.9417.18350.0329-0.0145-0.45230.86660.05751.1892-0.1089-0.8065-0.09030.6208-0.0680.55420.27-0.0050.576132.99811.20565.3608
104.4935-3.4099-1.90955.17091.38760.90640.1677-0.54550.14811.0635-0.0056-0.08550.02820.3692-0.16220.7704-0.1054-0.13930.4158-0.11990.121656.262913.632658.6396
116.10910.590.23724.7916-0.1895.73790.1780.5084-0.16150.3024-0.1648-0.75960.17820.816-0.01320.0410.0036-0.03660.3138-0.13080.266467.361242.753629.4319
123.26520.40592.2162.4396-0.23783.19920.2632-0.16050.51180.169-0.2890.1991-0.1452-0.03960.02580.1121-0.03260.10980.1181-0.12060.218844.446640.233736.723
135.89071.17210.66865.4511-0.8321.32960.11230.14390.38041.0191-0.1179-0.9871-0.28580.34520.00560.4988-0.1278-0.26480.4333-0.11020.356769.416920.57954.0701
144.2592-4.124-1.58217.9370.6910.80920.0486-0.47350.21571.11120.0134-0.089-0.18170.2148-0.0620.6876-0.11270.06990.2734-0.12890.069550.87924.817261.8809
156.1971-0.42481.11365.64740.73963.10230.0579-0.07130.0497-0.16050.0965-0.7073-0.00870.7003-0.15440.175-0.003-0.16010.412-0.00330.282973.2002-6.159743.6857
163.4915-1.0113-2.20562.81090.4174.24880.0683-0.1893-0.1770.63960.09150.3929-0.02120.0958-0.15980.2845-0.0633-0.01880.15050.06880.165649.5483-8.050547.4664
173.6916-0.1772-0.26873.17780.4014.19070.2596-0.2844-0.0291-0.1845-0.2446-0.0082-0.1038-0.0624-0.0150.1272-0.0279-0.14240.3508-0.05320.228565.4802-7.009412.5613
182.59241.5172-2.90374.6034-3.40944.05080.04110.1648-0.32010.1207-0.16510.225-0.0495-0.04010.1240.1985-0.0604-0.23270.3957-0.08040.417442.0648-6.264318.3559
194.2174-0.1051-1.78154.5253-0.61483.57220.3419-0.13090.14660.2559-0.165-0.0404-0.29960.1132-0.17690.1515-0.0077-0.14810.36180.00240.270362.864323.9423.9619
202.68351.94310.56783.37542.20652.29430.21150.38660.1840.02610.02930.28130.0163-0.1268-0.24090.14110.0924-0.14360.38820.03290.425239.799223.828811.3776
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 73
2X-RAY DIFFRACTION2A74 - 156
3X-RAY DIFFRACTION3B22 - 112
4X-RAY DIFFRACTION4B113 - 157
5X-RAY DIFFRACTION5C22 - 93
6X-RAY DIFFRACTION6C94 - 159
7X-RAY DIFFRACTION7D22 - 93
8X-RAY DIFFRACTION8D94 - 159
9X-RAY DIFFRACTION9E22 - 92
10X-RAY DIFFRACTION10E93 - 159
11X-RAY DIFFRACTION11F22 - 93
12X-RAY DIFFRACTION12F94 - 159
13X-RAY DIFFRACTION13G22 - 112
14X-RAY DIFFRACTION14G113 - 159
15X-RAY DIFFRACTION15H21 - 93
16X-RAY DIFFRACTION16H94 - 158
17X-RAY DIFFRACTION17I22 - 93
18X-RAY DIFFRACTION18I94 - 159
19X-RAY DIFFRACTION19J22 - 90
20X-RAY DIFFRACTION20J91 - 159

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