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- PDB-3m6a: Crystal structure of Bacillus subtilis Lon C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3m6a
TitleCrystal structure of Bacillus subtilis Lon C-terminal domain
ComponentsATP-dependent protease La 1Endopeptidase La
KeywordsHYDROLASE / alpha / beta / ATP-binding / nucleotide-binding / protease / serine protease / stress response
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / cellular response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5270 / Lon protease, bacterial / Lon protease, bacterial/eukaryotic-type / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon protease, N-terminal domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5270 / Lon protease, bacterial / Lon protease, bacterial/eukaryotic-type / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Helicase, Ruva Protein; domain 3 - #60 / Ribosomal Protein S5; domain 2 - #10 / PUA-like superfamily / Ribosomal Protein S5; domain 2 / Helicase, Ruva Protein; domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribosomal protein S5 domain 2-type fold, subgroup / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Lon protease 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsDuman, R.E. / Lowe, J.Y.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structures of Bacillus subtilis Lon Protease.
Authors: Duman, R.E. / Lowe, J.
History
DepositionMar 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent protease La 1
B: ATP-dependent protease La 1
C: ATP-dependent protease La 1
D: ATP-dependent protease La 1
E: ATP-dependent protease La 1
F: ATP-dependent protease La 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,79512
Polymers360,2326
Non-polymers2,5636
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ATP-dependent protease La 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4662
Polymers60,0391
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: ATP-dependent protease La 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4662
Polymers60,0391
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: ATP-dependent protease La 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4662
Polymers60,0391
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: ATP-dependent protease La 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4662
Polymers60,0391
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: ATP-dependent protease La 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4662
Polymers60,0391
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
F: ATP-dependent protease La 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4662
Polymers60,0391
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.382, 127.400, 148.993
Angle α, β, γ (deg.)90.00, 100.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
12
22
32
42
52
62
13
23
33
43
53
63
14
24
34
44
54
64

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 246:298 )
211chain B and (resseq 246:298 )
311chain C and (resseq 246:298 )
411chain D and (resseq 246:298 )
511chain E and (resseq 246:298 )
611chain F and (resseq 246:298 )
112chain A and (resseq 308:382 or resseq 403:427 or resseq 437:490 )
212chain B and (resseq 308:382 or resseq 403:427 or resseq 437:490 )
312chain C and (resseq 308:382 or resseq 403:427 or resseq 437:490 )
412chain D and (resseq 308:382 or resseq 403:427 or resseq 437:490 )
512chain E and (resseq 308:382 or resseq 403:427 or resseq 437:490 )
612chain F and (resseq 308:382 or resseq 403:427 or resseq 437:490 )
113chain A and (resseq 491:582 )
213chain B and (resseq 491:582 )
313chain C and (resseq 491:582 )
413chain D and (resseq 491:582 )
513chain E and (resseq 491:582 )
613chain F and (resseq 491:582 )
114chain A and (resseq 591:770 )
214chain B and (resseq 591:770 )
314chain C and (resseq 591:770 )
414chain D and (resseq 591:770 )
514chain E and (resseq 591:770 )
614chain F and (resseq 591:770 )

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
ATP-dependent protease La 1 / Endopeptidase La


Mass: 60038.691 Da / Num. of mol.: 6 / Fragment: C-terminal domain (240-774) / Mutation: S677A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU28200, lon, lonA / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: P37945, endopeptidase La
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium Citrate, 0.5M Ammonium Acetate, 14% PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9537,1.2546
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
21.25461
ReflectionResolution: 3.4→58.42 Å / Num. all: 52274 / Num. obs: 52431 / % possible obs: 99.7 % / Observed criterion σ(F): 1.3 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Rsym value: 0.105 / Net I/σ(I): 8
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.68 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASESphasing
PHENIX(phenix.refine: dev_249)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.4→29.915 Å / SU ML: 0.51 / Isotropic thermal model: isotropic / σ(F): 0.91 / Phase error: 33.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3127 5051 4.98 %
Rwork0.265 --
obs0.2673 101419 98.74 %
all-102713 -
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.2 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4017 Å20 Å27.917 Å2
2--6.68 Å2-0 Å2
3----8.0817 Å2
Refinement stepCycle: LAST / Resolution: 3.4→29.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23034 0 162 0 23196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123526
X-RAY DIFFRACTIONf_angle_d1.29831746
X-RAY DIFFRACTIONf_dihedral_angle_d17.4749030
X-RAY DIFFRACTIONf_chiral_restr0.0733714
X-RAY DIFFRACTIONf_plane_restr0.0044032
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A419X-RAY DIFFRACTIONPOSITIONAL
12B419X-RAY DIFFRACTIONPOSITIONAL0.018
13C419X-RAY DIFFRACTIONPOSITIONAL0.023
14D419X-RAY DIFFRACTIONPOSITIONAL0.017
15E419X-RAY DIFFRACTIONPOSITIONAL0.018
16F419X-RAY DIFFRACTIONPOSITIONAL0.015
21A1191X-RAY DIFFRACTIONPOSITIONAL
22B1191X-RAY DIFFRACTIONPOSITIONAL0.047
23C1191X-RAY DIFFRACTIONPOSITIONAL0.048
24D1191X-RAY DIFFRACTIONPOSITIONAL0.062
25E1191X-RAY DIFFRACTIONPOSITIONAL0.052
26F1191X-RAY DIFFRACTIONPOSITIONAL0.055
31A755X-RAY DIFFRACTIONPOSITIONAL
32B755X-RAY DIFFRACTIONPOSITIONAL0.067
33C755X-RAY DIFFRACTIONPOSITIONAL0.062
34D755X-RAY DIFFRACTIONPOSITIONAL0.068
35E755X-RAY DIFFRACTIONPOSITIONAL0.066
36F755X-RAY DIFFRACTIONPOSITIONAL0.065
41A1332X-RAY DIFFRACTIONPOSITIONAL
42B1332X-RAY DIFFRACTIONPOSITIONAL0.055
43C1332X-RAY DIFFRACTIONPOSITIONAL0.048
44D1332X-RAY DIFFRACTIONPOSITIONAL0.055
45E1332X-RAY DIFFRACTIONPOSITIONAL0.052
46F1332X-RAY DIFFRACTIONPOSITIONAL0.054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.43860.45492000.38213329X-RAY DIFFRACTION99
3.4386-3.4790.39922020.36463073X-RAY DIFFRACTION99
3.479-3.52130.41371530.36233229X-RAY DIFFRACTION99
3.5213-3.56580.41951690.35283322X-RAY DIFFRACTION99
3.5658-3.61270.41381830.35333108X-RAY DIFFRACTION99
3.6127-3.66210.38981740.34063265X-RAY DIFFRACTION99
3.6621-3.71430.34541530.30033243X-RAY DIFFRACTION99
3.7143-3.76970.37231720.28153194X-RAY DIFFRACTION99
3.7697-3.82840.32541870.27683293X-RAY DIFFRACTION99
3.8284-3.89110.32751460.28723182X-RAY DIFFRACTION99
3.8911-3.9580.38211740.28253240X-RAY DIFFRACTION99
3.958-4.02980.30021280.28163278X-RAY DIFFRACTION100
4.0298-4.10720.40581610.27173329X-RAY DIFFRACTION100
4.1072-4.19080.26231580.25193195X-RAY DIFFRACTION100
4.1908-4.28160.33562110.25243185X-RAY DIFFRACTION100
4.2816-4.38090.27171980.23413194X-RAY DIFFRACTION100
4.3809-4.49020.28821460.22743307X-RAY DIFFRACTION100
4.4902-4.61110.28611720.22533210X-RAY DIFFRACTION100
4.6111-4.74630.29941740.23543274X-RAY DIFFRACTION100
4.7463-4.89890.29311700.23363268X-RAY DIFFRACTION100
4.8989-5.07310.3061400.22473244X-RAY DIFFRACTION100
5.0731-5.27520.3041710.23763231X-RAY DIFFRACTION100
5.2752-5.51390.33381750.25983270X-RAY DIFFRACTION100
5.5139-5.80260.34921700.26653221X-RAY DIFFRACTION99
5.8026-6.16320.33341720.25863207X-RAY DIFFRACTION100
6.1632-6.63430.25641490.24563236X-RAY DIFFRACTION99
6.6343-7.29310.25951680.21873202X-RAY DIFFRACTION99
7.2931-8.32850.24441710.20433041X-RAY DIFFRACTION93
8.3285-10.41880.19891890.17483129X-RAY DIFFRACTION97
10.4188-29.91610.29031150.28062869X-RAY DIFFRACTION87
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)
11.4337-0.80421.12170.8947-0.68471.0105-0.36520.3841-0.36120.29451.2010.6748-0.5886-0.38120.04671.0648-0.7465-0.0956-0.0013-0.06392.197972.485920.638710.8574
20.2004-0.06640.09390.14530.09040.24720.4526-0.7108-0.2421-0.02910.9757-0.8724-0.07090.65130.03420.62280.0618-0.37681.24090.62571.884751.340627.717162.9904
30.0372-0.0354-0.0268-0.00520.00760.0107-0.3541-0.4732-0.6039-0.2634-0.98830.32930.97630.4469-0.00882.55890.5054-1.8842.2113-1.45623.237967.512139.375822.3854
40.085-0.0491-0.0509-0.03590.06780.0572-0.0821-0.15560.52890.6016-0.2198-1.1826-0.4738-0.5715-0.00291.1565-0.52280.212.43230.2211.85280.0296-1.876127.5791
50.04880.05140.00990.05920.05570.1489-0.3381-1.01820.99350.1511-0.7597-0.19550.46360.4009-0.01781.63940.2922-0.56732.0970.64091.927559.331140.805745.7838
60.09-0.14090.00570.2871-0.32360.52840.406-0.1883-0.48550.64081.35250.68391.1833-0.85060.04011.84690.2311-0.40861.3383-0.89761.989334.9449.501759.2042
70.9203-0.44590.30080.9632-1.04193.7430.28880.636-0.46780.7214-0.1914-0.18040.1572-0.14551.16830.60040.0292-0.18970.1861-0.31230.709341.053318.08651.5604
84.33370.5684-1.38753.00430.71381.98910.51990.07940.9951-0.4347-0.2923-0.1202-0.41430.2834-1.49150.6257-0.3547-0.01470.29530.10120.366625.09344.490374.1573
91.87880.64421.33441.6301-0.55918.01541.52851.0653-0.48961.16440.23950.68590.9704-0.21522.72240.7290.1924-0.03990.6681-0.274-0.176337.665450.555412.5794
100.92940.19210.35221.86410.85561.13310.40310.5401-0.4784-0.66290.14290.0177-1.62530.27531.21651.0815-0.2446-0.0809-0.0670.0320.361948.4842-10.688221.0301
110.4232-0.1715-0.60031.62630.36790.60351.0490.5680.2049-0.1616-1.25750.73190.2098-0.0062-0.09811.1904-0.09360.31340.14360.65210.234233.53560.787844.6116
120.5691-0.2915-0.36451.14750.08430.7255-0.0816-0.2372-0.47640.04750.03920.30930.0391-0.31120.14120.744-0.73180.14961.3616-0.65340.782610.128612.640780.1744
131.9960.5634-0.60963.208-2.28922.1960.6964-0.58550.9530.9922.21773.4918-0.2971-1.09364.68780.2635-0.6419-1.2388-0.3949-1.1333-1.200629.5518-12.07732.6677
140.5834-0.096-0.33130.2927-1.25412.8760.33420.8085-0.54490.54640.25780.1113-2.1268-1.0273-0.07571.5365-0.32880.27520.0360.13390.573121.218674.600762.4534
151.9259-1.8423-0.37623.4441.61731.9346-0.096-0.0725-0.8707-0.5793-0.55352.21120.3548-0.1001-0.47370.5088-0.0136-0.36330.76760.17440.08524.351433.2839-11.3844
161.111-0.54031.34481.2961-0.62133.0279-0.3894-1.54220.06580.2870.5969-0.04290.4599-2.4195-0.28540.56040.24260.156-0.11150.52980.419739.3426-28.387145.5552
170.79780.2721.08930.63481.09594.82830.0684-0.6521-0.2459-0.441-0.5431-0.3506-0.4713-2.2207-0.30570.88320.27920.19660.22910.44610.534124.463272.230615.5734
182.13980.86590.52670.81290.18880.42690.21411.77370.19090.61530.53850.9485-0.46230.00590.08250.5745-0.24950.08190.59420.07630.11718.656341.632194.5557
192.06660.5092-0.68363.75871.13811.79930.1540.83330.36860.02280.72240.02440.0324-0.56510.81040.18960.2217-0.26590.7380.16320.70933.502812.667414.1358
201.12420.5984-0.21961.78710.31291.03640.3971-0.7271-0.10440.4253-0.4538-0.54890.6171-1.08750.03790.487-0.05240.16711.33880.21970.5229-11.5856.867865.4298
210.6750.1652-0.08281.73430.4192.38910.18510.01380.24960.2933-0.04690.11620.04550.68740.02970.25270.28950.07080.69440.26630.5463-1.486942.534313.7403
221.4668-0.49590.92761.1945-0.60981.1257-1.0768-1.0735-0.18320.8430.5821-0.0805-1.3688-0.4152-0.13280.60080.6178-0.01281.11890.14510.435611.9933-4.944336.792
230.27310.16820.31521.3210.49570.684-0.3462-0.5045-0.3153-0.5356-0.2085-0.25920.30520.0052-0.00980.49180.450.29120.84720.23520.549-5.222361.70736.4908
241.1083-0.70680.65121.16720.57840.729-1.00980.7342-0.87890.28780.61450.2105-0.7220.5195-0.09240.2361-0.48330.18071.41420.09540.7405-24.263933.285379.883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A AND resseq 246:298
2X-RAY DIFFRACTION2chain B AND resseq 246:298
3X-RAY DIFFRACTION3chain C AND resseq 246:298
4X-RAY DIFFRACTION4chain D AND resseq 246:298
5X-RAY DIFFRACTION5chain E AND resseq 246:298
6X-RAY DIFFRACTION6chain F AND resseq 246:298
7X-RAY DIFFRACTION7chain A AND resseq 308:490
8X-RAY DIFFRACTION8chain B AND resseq 308:490
9X-RAY DIFFRACTION9chain C AND resseq 308:490
10X-RAY DIFFRACTION10chain D AND resseq 308:490
11X-RAY DIFFRACTION11chain E AND resseq 308:490
12X-RAY DIFFRACTION12chain F AND resseq 308:490
13X-RAY DIFFRACTION13chain A AND resseq 491:582
14X-RAY DIFFRACTION14chain B AND resseq 491:582
15X-RAY DIFFRACTION15chain C AND resseq 491:582
16X-RAY DIFFRACTION16chain D AND resseq 491:582
17X-RAY DIFFRACTION17chain E AND resseq 491:582
18X-RAY DIFFRACTION18chain F AND resseq 491:582
19X-RAY DIFFRACTION19chain A AND resseq 591:770
20X-RAY DIFFRACTION20chain B AND resseq 591:770
21X-RAY DIFFRACTION21chain C AND resseq 591:770
22X-RAY DIFFRACTION22chain D AND resseq 591:770
23X-RAY DIFFRACTION23chain E AND resseq 591:770
24X-RAY DIFFRACTION24chain F AND resseq 591:770

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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

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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

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