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- PDB-8joh: structure of Echinococcus multilocularis Cystatin B -

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Basic information

Entry
Database: PDB / ID: 8joh
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: 2.04 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
DepositionJun 7, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 12, 2024Provider: 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
Water00
1
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-70 kcal/mol
Surface area19720 Å2
MethodPISA
2
A: Cystatin B Stefin B
D: Cystatin B Stefin B


Theoretical massNumber of molelcules
Total (without water)23,9972
Polymers23,9972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-25 kcal/mol
Surface area10540 Å2
MethodPISA
3
B: Cystatin B Stefin B
F: Cystatin B Stefin B


Theoretical massNumber of molelcules
Total (without water)23,9972
Polymers23,9972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-27 kcal/mol
Surface area10450 Å2
MethodPISA
4
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-71 kcal/mol
Surface area19160 Å2
MethodPISA
5
C: Cystatin B Stefin B
G: Cystatin B Stefin B


Theoretical massNumber of molelcules
Total (without water)23,9972
Polymers23,9972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-25 kcal/mol
Surface area10060 Å2
MethodPISA
6
E: Cystatin B Stefin B
H: Cystatin B Stefin B


Theoretical massNumber of molelcules
Total (without water)23,9972
Polymers23,9972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-27 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.720, 65.990, 92.710
Angle α, β, γ (deg.)90.000, 103.381, 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
322METMETGLUGLUAA3 - 1003 - 100
422METMETGLUGLUDC3 - 1003 - 100
533METMETHISHISAA3 - 1013 - 101
633METMETHISHISFD3 - 1013 - 101
744METMETHISHISAA3 - 1023 - 102
844METMETHISHISCE3 - 1023 - 102
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
191010CYSCYSHISHISBB4 - 1014 - 101
201010CYSCYSHISHISCE4 - 1014 - 101
211111CYSCYSGLUGLUBB4 - 1004 - 100
221111CYSCYSGLUGLUEF4 - 1004 - 100
231212CYSCYSHISHISBB4 - 1014 - 101
241212CYSCYSHISHISGG4 - 1014 - 101
251313CYSCYSHISHISBB4 - 1014 - 101
261313CYSCYSHISHISHH4 - 1014 - 101
271414METMETGLUGLUDC3 - 1003 - 100
281414METMETGLUGLUFD3 - 1003 - 100
291515METMETHISHISDC3 - 1013 - 101
301515METMETHISHISCE3 - 1013 - 101
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 - 1023 - 102
462323METMETHISHISEF3 - 1023 - 102
472424CYSCYSHISHISCE4 - 1014 - 101
482424CYSCYSHISHISGG4 - 1014 - 101
492525CYSCYSHISHISCE4 - 1014 - 101
502525CYSCYSHISHISHH4 - 1014 - 101
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

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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: 2.25 Å3/Da / Density % sol: 45.44 %
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: 2.04→53.314 Å / Num. obs: 54430 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.997 / Net I/σ(I): 11.6
Reflection shellResolution: 2.04→2.09 Å / Num. unique obs: 4003 / CC1/2: 0.758

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→53.314 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.288 / WRfactor Rwork: 0.255 / SU B: 6.821 / SU ML: 0.178 / Average fsc free: 0.8383 / Average fsc work: 0.8555 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.203
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2816 2726 5.015 %
Rwork0.2497 51631 -
all0.251 --
obs-54357 99.489 %
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: 47.393 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å20 Å2-0.141 Å2
2--4.135 Å20 Å2
3----1.211 Å2
Refinement stepCycle: LAST / Resolution: 2.04→53.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6219 0 0 0 6219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136376
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155892
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.648659
X-RAY DIFFRACTIONr_angle_other_deg1.3051.58113622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9735781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25222.823333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.098151064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9581532
X-RAY DIFFRACTIONr_chiral_restr0.0820.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021380
X-RAY DIFFRACTIONr_nbd_refined0.2170.21044
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.25140
X-RAY DIFFRACTIONr_nbtor_refined0.1510.22946
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23299
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.279
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.218
X-RAY DIFFRACTIONr_nbd_other0.2990.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2260.210
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0480.21
X-RAY DIFFRACTIONr_mcbond_it3.8624.7453151
X-RAY DIFFRACTIONr_mcbond_other3.8624.7453150
X-RAY DIFFRACTIONr_mcangle_it5.557.13923
X-RAY DIFFRACTIONr_mcangle_other5.5497.13924
X-RAY DIFFRACTIONr_scbond_it5.2725.2863225
X-RAY DIFFRACTIONr_scbond_other5.2715.2863226
X-RAY DIFFRACTIONr_scangle_it7.7567.7024736
X-RAY DIFFRACTIONr_scangle_other7.7557.7024737
X-RAY DIFFRACTIONr_lrange_it10.96890.27122824
X-RAY DIFFRACTIONr_lrange_other10.96890.26922825
X-RAY DIFFRACTIONr_ncsr_local_group_10.1260.052533
X-RAY DIFFRACTIONr_ncsr_local_group_20.150.052515
X-RAY DIFFRACTIONr_ncsr_local_group_30.1480.052582
X-RAY DIFFRACTIONr_ncsr_local_group_40.1410.052456
X-RAY DIFFRACTIONr_ncsr_local_group_50.1370.052596
X-RAY DIFFRACTIONr_ncsr_local_group_60.2150.052262
X-RAY DIFFRACTIONr_ncsr_local_group_70.1420.052497
X-RAY DIFFRACTIONr_ncsr_local_group_80.1350.052552
X-RAY DIFFRACTIONr_ncsr_local_group_90.1440.052524
X-RAY DIFFRACTIONr_ncsr_local_group_100.1340.052442
X-RAY DIFFRACTIONr_ncsr_local_group_110.0820.052672
X-RAY DIFFRACTIONr_ncsr_local_group_120.2010.052382
X-RAY DIFFRACTIONr_ncsr_local_group_130.1330.052552
X-RAY DIFFRACTIONr_ncsr_local_group_140.1410.052577
X-RAY DIFFRACTIONr_ncsr_local_group_150.1460.052428
X-RAY DIFFRACTIONr_ncsr_local_group_160.1340.052560
X-RAY DIFFRACTIONr_ncsr_local_group_170.1870.052392
X-RAY DIFFRACTIONr_ncsr_local_group_180.1210.052554
X-RAY DIFFRACTIONr_ncsr_local_group_190.1470.052488
X-RAY DIFFRACTIONr_ncsr_local_group_200.1550.052570
X-RAY DIFFRACTIONr_ncsr_local_group_210.1970.052379
X-RAY DIFFRACTIONr_ncsr_local_group_220.1060.052645
X-RAY DIFFRACTIONr_ncsr_local_group_230.1390.052482
X-RAY DIFFRACTIONr_ncsr_local_group_240.2090.052231
X-RAY DIFFRACTIONr_ncsr_local_group_250.1330.052454
X-RAY DIFFRACTIONr_ncsr_local_group_260.2050.052350
X-RAY DIFFRACTIONr_ncsr_local_group_270.1310.052535
X-RAY DIFFRACTIONr_ncsr_local_group_280.1990.052403
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.125550.05007
12BX-RAY DIFFRACTIONLocal ncs0.125550.05007
23AX-RAY DIFFRACTIONLocal ncs0.149950.05007
24DX-RAY DIFFRACTIONLocal ncs0.149950.05007
35AX-RAY DIFFRACTIONLocal ncs0.147690.05007
36FX-RAY DIFFRACTIONLocal ncs0.147690.05007
47AX-RAY DIFFRACTIONLocal ncs0.140960.05007
48CX-RAY DIFFRACTIONLocal ncs0.140960.05007
59AX-RAY DIFFRACTIONLocal ncs0.136620.05007
510EX-RAY DIFFRACTIONLocal ncs0.136620.05007
611AX-RAY DIFFRACTIONLocal ncs0.214780.05006
612GX-RAY DIFFRACTIONLocal ncs0.214780.05006
713AX-RAY DIFFRACTIONLocal ncs0.142050.05007
714HX-RAY DIFFRACTIONLocal ncs0.142050.05007
815BX-RAY DIFFRACTIONLocal ncs0.135370.05008
816DX-RAY DIFFRACTIONLocal ncs0.135370.05008
917BX-RAY DIFFRACTIONLocal ncs0.143630.05008
918FX-RAY DIFFRACTIONLocal ncs0.143630.05008
1019BX-RAY DIFFRACTIONLocal ncs0.13430.05009
1020CX-RAY DIFFRACTIONLocal ncs0.13430.05009
1121BX-RAY DIFFRACTIONLocal ncs0.081660.05008
1122EX-RAY DIFFRACTIONLocal ncs0.081660.05008
1223BX-RAY DIFFRACTIONLocal ncs0.200910.05008
1224GX-RAY DIFFRACTIONLocal ncs0.200910.05008
1325BX-RAY DIFFRACTIONLocal ncs0.133010.05008
1326HX-RAY DIFFRACTIONLocal ncs0.133010.05008
1427DX-RAY DIFFRACTIONLocal ncs0.140720.05008
1428FX-RAY DIFFRACTIONLocal ncs0.140720.05008
1529DX-RAY DIFFRACTIONLocal ncs0.145570.05008
1530CX-RAY DIFFRACTIONLocal ncs0.145570.05008
1631DX-RAY DIFFRACTIONLocal ncs0.13390.05007
1632EX-RAY DIFFRACTIONLocal ncs0.13390.05007
1733DX-RAY DIFFRACTIONLocal ncs0.186870.05007
1734GX-RAY DIFFRACTIONLocal ncs0.186870.05007
1835DX-RAY DIFFRACTIONLocal ncs0.121240.05007
1836HX-RAY DIFFRACTIONLocal ncs0.121240.05007
1937FX-RAY DIFFRACTIONLocal ncs0.146910.05008
1938CX-RAY DIFFRACTIONLocal ncs0.146910.05008
2039FX-RAY DIFFRACTIONLocal ncs0.154630.05007
2040EX-RAY DIFFRACTIONLocal ncs0.154630.05007
2141FX-RAY DIFFRACTIONLocal ncs0.197490.05008
2142GX-RAY DIFFRACTIONLocal ncs0.197490.05008
2243FX-RAY DIFFRACTIONLocal ncs0.105730.05008
2244HX-RAY DIFFRACTIONLocal ncs0.105730.05008
2345CX-RAY DIFFRACTIONLocal ncs0.139130.05008
2346EX-RAY DIFFRACTIONLocal ncs0.139130.05008
2447CX-RAY DIFFRACTIONLocal ncs0.209420.05008
2448GX-RAY DIFFRACTIONLocal ncs0.209420.05008
2549CX-RAY DIFFRACTIONLocal ncs0.133270.05008
2550HX-RAY DIFFRACTIONLocal ncs0.133270.05008
2651EX-RAY DIFFRACTIONLocal ncs0.205090.05007
2652GX-RAY DIFFRACTIONLocal ncs0.205090.05007
2753EX-RAY DIFFRACTIONLocal ncs0.131310.05007
2754HX-RAY DIFFRACTIONLocal ncs0.131310.05007
2855GX-RAY DIFFRACTIONLocal ncs0.199020.05007
2856HX-RAY DIFFRACTIONLocal ncs0.199020.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.0930.3522270.3313774X-RAY DIFFRACTION99.5026
2.093-2.150.3521940.313717X-RAY DIFFRACTION99.4659
2.15-2.2130.3541920.333607X-RAY DIFFRACTION99.7899
2.213-2.2810.4131890.4023466X-RAY DIFFRACTION98.3585
2.281-2.3550.3711680.3133373X-RAY DIFFRACTION99.6342
2.355-2.4380.3171510.2853299X-RAY DIFFRACTION99.9131
2.438-2.530.3441660.2773201X-RAY DIFFRACTION99.8517
2.53-2.6330.3461730.2883024X-RAY DIFFRACTION99.8438
2.633-2.750.3281630.282925X-RAY DIFFRACTION99.5166
2.75-2.8840.3051370.2622823X-RAY DIFFRACTION99.5962
2.884-3.040.2681280.2612675X-RAY DIFFRACTION99.6091
3.04-3.2240.3031460.2552504X-RAY DIFFRACTION99.5866
3.224-3.4470.3051230.2612410X-RAY DIFFRACTION99.8423
3.447-3.7220.3221000.2462227X-RAY DIFFRACTION99.7428
3.722-4.0770.2491190.2282047X-RAY DIFFRACTION99.8157
4.077-4.5570.2061000.1821856X-RAY DIFFRACTION99.6434
4.557-5.260.172850.171614X-RAY DIFFRACTION98.7791
5.26-6.4360.27740.2221391X-RAY DIFFRACTION99.1875
6.436-9.0790.215670.2161079X-RAY DIFFRACTION98.7931
8-80.339240.266619X-RAY DIFFRACTION96.1136

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