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- PDB-9uoz: Structure of Echinococcus multilocularis Cystatin B -

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Basic information

Entry
Database: PDB / ID: 9uoz
TitleStructure of Echinococcus multilocularis Cystatin B
ComponentsCystatin B Stefin B
KeywordsHYDROLASE / Inhibitor
Function / homologyProteinase inhibitor I25A, stefin / Cystatin domain / Cystatin domain / Cystatin superfamily / cysteine-type endopeptidase inhibitor activity / cytosol / Cystatin B Stefin B
Function and homology information
Biological speciesEchinococcus multilocularis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsHuang, S.Q. / Hong, W.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal Structure of Echinococcus multilocularis Cystatin B
Authors: Huang, S.Q. / Hong, W.B.
History
DepositionApr 27, 2025Deposition site: PDBJ / Processing site: PDBC
SupersessionAug 20, 2025ID: 8JOH
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystatin B Stefin B
B: Cystatin B Stefin B
D: Cystatin B Stefin B
F: Cystatin B Stefin B
C: Cystatin B Stefin B
E: Cystatin B Stefin B
G: Cystatin B Stefin B
H: Cystatin B Stefin B


Theoretical massNumber of molelcules
Total (without water)95,9898
Polymers95,9898
Non-polymers00
Water6,503361
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cystatin B Stefin B
B: Cystatin B Stefin B
D: Cystatin B Stefin B
F: Cystatin B Stefin B


Theoretical massNumber of molelcules
Total (without water)47,9944
Polymers47,9944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-68 kcal/mol
Surface area19910 Å2
MethodPISA
3
A: Cystatin B Stefin B
D: Cystatin B Stefin B


Theoretical massNumber of molelcules
Total (without water)23,9972
Polymers23,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-23 kcal/mol
Surface area10850 Å2
MethodPISA
4
B: Cystatin B Stefin B
F: Cystatin B Stefin B


Theoretical massNumber of molelcules
Total (without water)23,9972
Polymers23,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-24 kcal/mol
Surface area10460 Å2
MethodPISA
5
C: Cystatin B Stefin B
E: Cystatin B Stefin B
G: Cystatin B Stefin B
H: Cystatin B Stefin B


Theoretical massNumber of molelcules
Total (without water)47,9944
Polymers47,9944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11040 Å2
ΔGint-70 kcal/mol
Surface area19510 Å2
MethodPISA
6
C: Cystatin B Stefin B
G: Cystatin B Stefin B


Theoretical massNumber of molelcules
Total (without water)23,9972
Polymers23,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-23 kcal/mol
Surface area10330 Å2
MethodPISA
7
E: Cystatin B Stefin B
H: Cystatin B Stefin B


Theoretical massNumber of molelcules
Total (without water)23,9972
Polymers23,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-27 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.773, 66.112, 92.600
Angle α, β, γ (deg.)90.000, 103.432, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42D
53A
63F
74A
84C
95A
105E
116A
126G
137A
147H
158B
168D
179B
189F
1910B
2010C
2111B
2211E
2312B
2412G
2513B
2613H
2714D
2814F
2915D
3015C
3116D
3216E
3317D
3417G
3518D
3618H
3719F
3819C
3920F
4020E
4121F
4221G
4322F
4422H
4523C
4623E
4724C
4824G
4925C
5025H
5126E
5226G
5327E
5427H
5528G
5628H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111CYSCYSGLUGLUAA4 - 1004 - 100
211CYSCYSGLUGLUBB4 - 1004 - 100
322PROPROGLUGLUAA2 - 1002 - 100
422PROPROGLUGLUDC2 - 1002 - 100
533METMETHISHISAA3 - 1013 - 101
633METMETHISHISFD3 - 1013 - 101
744METMETHISHISAA3 - 1013 - 101
844METMETHISHISCE3 - 1013 - 101
955METMETHISHISAA3 - 1023 - 102
1055METMETHISHISEF3 - 1023 - 102
1166CYSCYSGLUGLUAA4 - 1004 - 100
1266CYSCYSGLUGLUGG4 - 1004 - 100
1377CYSCYSGLUGLUAA4 - 1004 - 100
1477CYSCYSGLUGLUHH4 - 1004 - 100
1588CYSCYSGLUGLUBB4 - 1004 - 100
1688CYSCYSGLUGLUDC4 - 1004 - 100
1799CYSCYSGLUGLUBB4 - 1004 - 100
1899CYSCYSGLUGLUFD4 - 1004 - 100
191010CYSCYSGLUGLUBB4 - 1004 - 100
201010CYSCYSGLUGLUCE4 - 1004 - 100
211111CYSCYSGLUGLUBB4 - 1004 - 100
221111CYSCYSGLUGLUEF4 - 1004 - 100
231212CYSCYSHISHISBB4 - 1014 - 101
241212CYSCYSHISHISGG4 - 1014 - 101
251313CYSCYSHISHISBB4 - 1014 - 101
261313CYSCYSHISHISHH4 - 1014 - 101
271414METMETGLUGLUDC3 - 1003 - 100
281414METMETGLUGLUFD3 - 1003 - 100
291515METMETGLUGLUDC3 - 1003 - 100
301515METMETGLUGLUCE3 - 1003 - 100
311616METMETGLUGLUDC3 - 1003 - 100
321616METMETGLUGLUEF3 - 1003 - 100
331717CYSCYSGLUGLUDC4 - 1004 - 100
341717CYSCYSGLUGLUGG4 - 1004 - 100
351818CYSCYSGLUGLUDC4 - 1004 - 100
361818CYSCYSGLUGLUHH4 - 1004 - 100
371919METMETHISHISFD3 - 1023 - 102
381919METMETHISHISCE3 - 1023 - 102
392020METMETHISHISFD3 - 1013 - 101
402020METMETHISHISEF3 - 1013 - 101
412121CYSCYSGLUGLUFD4 - 1004 - 100
422121CYSCYSGLUGLUGG4 - 1004 - 100
432222CYSCYSGLUGLUFD4 - 1004 - 100
442222CYSCYSGLUGLUHH4 - 1004 - 100
452323METMETHISHISCE3 - 1013 - 101
462323METMETHISHISEF3 - 1013 - 101
472424CYSCYSGLUGLUCE4 - 1004 - 100
482424CYSCYSGLUGLUGG4 - 1004 - 100
492525CYSCYSGLUGLUCE4 - 1004 - 100
502525CYSCYSGLUGLUHH4 - 1004 - 100
512626CYSCYSGLUGLUEF4 - 1004 - 100
522626CYSCYSGLUGLUGG4 - 1004 - 100
532727CYSCYSGLUGLUEF4 - 1004 - 100
542727CYSCYSGLUGLUHH4 - 1004 - 100
552828CYSCYSHISHISGG4 - 1014 - 101
562828CYSCYSHISHISHH4 - 1014 - 101

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56

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Components

#1: Protein
Cystatin B Stefin B


Mass: 11998.584 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinococcus multilocularis (invertebrata)
Gene: EmuJ_000159200 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A087VZV0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 30% PEG400 100 mM Tris base/ Hydrochloric acid pH 8.5 200 mM Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. obs: 57418 / % possible obs: 98.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 29.371
Reflection shellResolution: 1.999→2.03 Å / Num. unique obs: 4125 / CC1/2: 0.822

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→37.247 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.592 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.171
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2405 2798 4.874 %
Rwork0.2107 54603 -
all0.212 --
obs-57401 98.812 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.232 Å2
Baniso -1Baniso -2Baniso -3
1--2.656 Å2-0 Å20.3 Å2
2--4.918 Å2-0 Å2
3----2.158 Å2
Refinement stepCycle: LAST / Resolution: 1.999→37.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 0 361 6637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126448
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165948
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.8388761
X-RAY DIFFRACTIONr_angle_other_deg0.6311.76913762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.375792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.083532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.462101071
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.68910304
X-RAY DIFFRACTIONr_chiral_restr0.10.2975
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027520
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021393
X-RAY DIFFRACTIONr_nbd_refined0.2250.21197
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.25300
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23039
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.23746
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1040.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1780.216
X-RAY DIFFRACTIONr_nbd_other0.2280.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.215
X-RAY DIFFRACTIONr_mcbond_it3.7444.1143189
X-RAY DIFFRACTIONr_mcbond_other3.7444.1143189
X-RAY DIFFRACTIONr_mcangle_it5.5477.3663974
X-RAY DIFFRACTIONr_mcangle_other5.5467.3663975
X-RAY DIFFRACTIONr_scbond_it5.294.7423259
X-RAY DIFFRACTIONr_scbond_other5.2894.7423260
X-RAY DIFFRACTIONr_scangle_it8.2268.3894787
X-RAY DIFFRACTIONr_scangle_other8.2258.3884788
X-RAY DIFFRACTIONr_lrange_it10.97150.62223824
X-RAY DIFFRACTIONr_lrange_other10.97650.54623649
X-RAY DIFFRACTIONr_ncsr_local_group_10.1250.052601
X-RAY DIFFRACTIONr_ncsr_local_group_20.140.052627
X-RAY DIFFRACTIONr_ncsr_local_group_30.1290.052668
X-RAY DIFFRACTIONr_ncsr_local_group_40.1240.052672
X-RAY DIFFRACTIONr_ncsr_local_group_50.1350.052673
X-RAY DIFFRACTIONr_ncsr_local_group_60.1930.052370
X-RAY DIFFRACTIONr_ncsr_local_group_70.1240.052603
X-RAY DIFFRACTIONr_ncsr_local_group_80.1220.052602
X-RAY DIFFRACTIONr_ncsr_local_group_90.1230.052583
X-RAY DIFFRACTIONr_ncsr_local_group_100.1160.052607
X-RAY DIFFRACTIONr_ncsr_local_group_110.0670.052733
X-RAY DIFFRACTIONr_ncsr_local_group_120.1770.052453
X-RAY DIFFRACTIONr_ncsr_local_group_130.1060.052635
X-RAY DIFFRACTIONr_ncsr_local_group_140.1270.052630
X-RAY DIFFRACTIONr_ncsr_local_group_150.1250.052630
X-RAY DIFFRACTIONr_ncsr_local_group_160.1290.052624
X-RAY DIFFRACTIONr_ncsr_local_group_170.1680.052478
X-RAY DIFFRACTIONr_ncsr_local_group_180.1090.052628
X-RAY DIFFRACTIONr_ncsr_local_group_190.1260.052723
X-RAY DIFFRACTIONr_ncsr_local_group_200.1310.052638
X-RAY DIFFRACTIONr_ncsr_local_group_210.180.052446
X-RAY DIFFRACTIONr_ncsr_local_group_220.0910.052719
X-RAY DIFFRACTIONr_ncsr_local_group_230.1210.052671
X-RAY DIFFRACTIONr_ncsr_local_group_240.1860.052425
X-RAY DIFFRACTIONr_ncsr_local_group_250.1080.052638
X-RAY DIFFRACTIONr_ncsr_local_group_260.1830.052417
X-RAY DIFFRACTIONr_ncsr_local_group_270.120.052583
X-RAY DIFFRACTIONr_ncsr_local_group_280.1710.052472
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.124830.05008
12BX-RAY DIFFRACTIONLocal ncs0.124830.05008
23AX-RAY DIFFRACTIONLocal ncs0.140170.05008
24DX-RAY DIFFRACTIONLocal ncs0.140170.05008
35AX-RAY DIFFRACTIONLocal ncs0.129150.05008
36FX-RAY DIFFRACTIONLocal ncs0.129150.05008
47AX-RAY DIFFRACTIONLocal ncs0.12370.05009
48CX-RAY DIFFRACTIONLocal ncs0.12370.05009
59AX-RAY DIFFRACTIONLocal ncs0.135050.05008
510EX-RAY DIFFRACTIONLocal ncs0.135050.05008
611AX-RAY DIFFRACTIONLocal ncs0.193250.05008
612GX-RAY DIFFRACTIONLocal ncs0.193250.05008
713AX-RAY DIFFRACTIONLocal ncs0.123770.05008
714HX-RAY DIFFRACTIONLocal ncs0.123770.05008
815BX-RAY DIFFRACTIONLocal ncs0.122180.05009
816DX-RAY DIFFRACTIONLocal ncs0.122180.05009
917BX-RAY DIFFRACTIONLocal ncs0.123020.05008
918FX-RAY DIFFRACTIONLocal ncs0.123020.05008
1019BX-RAY DIFFRACTIONLocal ncs0.115710.05009
1020CX-RAY DIFFRACTIONLocal ncs0.115710.05009
1121BX-RAY DIFFRACTIONLocal ncs0.067040.05009
1122EX-RAY DIFFRACTIONLocal ncs0.067040.05009
1223BX-RAY DIFFRACTIONLocal ncs0.177170.05008
1224GX-RAY DIFFRACTIONLocal ncs0.177170.05008
1325BX-RAY DIFFRACTIONLocal ncs0.105820.05009
1326HX-RAY DIFFRACTIONLocal ncs0.105820.05009
1427DX-RAY DIFFRACTIONLocal ncs0.127380.05009
1428FX-RAY DIFFRACTIONLocal ncs0.127380.05009
1529DX-RAY DIFFRACTIONLocal ncs0.124710.05009
1530CX-RAY DIFFRACTIONLocal ncs0.124710.05009
1631DX-RAY DIFFRACTIONLocal ncs0.128780.05009
1632EX-RAY DIFFRACTIONLocal ncs0.128780.05009
1733DX-RAY DIFFRACTIONLocal ncs0.16770.05009
1734GX-RAY DIFFRACTIONLocal ncs0.16770.05009
1835DX-RAY DIFFRACTIONLocal ncs0.108740.05009
1836HX-RAY DIFFRACTIONLocal ncs0.108740.05009
1937FX-RAY DIFFRACTIONLocal ncs0.125630.05009
1938CX-RAY DIFFRACTIONLocal ncs0.125630.05009
2039FX-RAY DIFFRACTIONLocal ncs0.130620.05009
2040EX-RAY DIFFRACTIONLocal ncs0.130620.05009
2141FX-RAY DIFFRACTIONLocal ncs0.180490.05008
2142GX-RAY DIFFRACTIONLocal ncs0.180490.05008
2243FX-RAY DIFFRACTIONLocal ncs0.091250.05009
2244HX-RAY DIFFRACTIONLocal ncs0.091250.05009
2345CX-RAY DIFFRACTIONLocal ncs0.121370.05009
2346EX-RAY DIFFRACTIONLocal ncs0.121370.05009
2447CX-RAY DIFFRACTIONLocal ncs0.185530.05008
2448GX-RAY DIFFRACTIONLocal ncs0.185530.05008
2549CX-RAY DIFFRACTIONLocal ncs0.108410.05009
2550HX-RAY DIFFRACTIONLocal ncs0.108410.05009
2651EX-RAY DIFFRACTIONLocal ncs0.183330.05008
2652GX-RAY DIFFRACTIONLocal ncs0.183330.05008
2753EX-RAY DIFFRACTIONLocal ncs0.119830.05008
2754HX-RAY DIFFRACTIONLocal ncs0.119830.05008
2855GX-RAY DIFFRACTIONLocal ncs0.171160.05008
2856HX-RAY DIFFRACTIONLocal ncs0.171160.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.0510.331830.2873633X-RAY DIFFRACTION89.7882
2.051-2.1070.2921860.2723796X-RAY DIFFRACTION96.4398
2.107-2.1670.3131910.2683786X-RAY DIFFRACTION98.8566
2.167-2.2340.2841880.253755X-RAY DIFFRACTION99.6966
2.234-2.3070.2951790.2623609X-RAY DIFFRACTION99.8419
2.307-2.3880.2771880.2253491X-RAY DIFFRACTION100
2.388-2.4770.2391750.2233382X-RAY DIFFRACTION100
2.477-2.5780.2671710.2333269X-RAY DIFFRACTION100
2.578-2.6920.2931660.2383120X-RAY DIFFRACTION100
2.692-2.8230.2411450.2232997X-RAY DIFFRACTION99.9682
2.823-2.9740.2461480.2142849X-RAY DIFFRACTION99.9666
2.974-3.1540.2411480.2122712X-RAY DIFFRACTION99.9301
3.154-3.370.2441360.2072508X-RAY DIFFRACTION100
3.37-3.6370.2391320.2022384X-RAY DIFFRACTION100
3.637-3.980.2381210.192169X-RAY DIFFRACTION99.9127
3.98-4.4440.162940.1621985X-RAY DIFFRACTION99.6644
4.444-5.1190.172800.151774X-RAY DIFFRACTION99.6774
5.119-6.240.229660.2081503X-RAY DIFFRACTION99.5558
6.24-8.7040.268660.2111178X-RAY DIFFRACTION99.8395
8.704-37.2470.19350.19703X-RAY DIFFRACTION99.0604

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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

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