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- PDB-3zn5: VP16, a capsid protein of bacteriophage P23-77 (VP16-virus-derived) -

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Basic information

Entry
Database: PDB / ID: 3zn5
TitleVP16, a capsid protein of bacteriophage P23-77 (VP16-virus-derived)
ComponentsVP16
KeywordsVIRAL PROTEIN
Function / homologyJelly Rolls - #1180 / : / Major capsid protein VP16-like / Jelly Rolls / Sandwich / Mainly Beta / identical protein binding / VP16
Function and homology information
Biological speciesTHERMUS PHAGE P23-77 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsRissanen, I. / Grimes, J.M. / Pawlowski, A. / Mantynen, S. / Harlos, K. / Bamford, J.K.H. / Stuart, D.I.
CitationJournal: Structure / Year: 2013
Title: Bacteriophage P23-77 Capsid Protein Structures Reveal the Archetype of an Ancient Branch from a Major Virus Lineage.
Authors: Rissanen, I. / Grimes, J.M. / Pawlowski, A. / Mantynen, S. / Harlos, K. / Bamford, J.K.H. / Stuart, D.I.
History
DepositionFeb 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: VP16
B: VP16
C: VP16
D: VP16
E: VP16
F: VP16
G: VP16
H: VP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,16412
Polymers153,0228
Non-polymers1424
Water6,269348
1
E: VP16
F: VP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2913
Polymers38,2562
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-43.9 kcal/mol
Surface area15500 Å2
MethodPISA
2
A: VP16
B: VP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2913
Polymers38,2562
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-43.7 kcal/mol
Surface area15870 Å2
MethodPISA
3
G: VP16
H: VP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2913
Polymers38,2562
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-44.6 kcal/mol
Surface area15130 Å2
MethodPISA
4
C: VP16
D: VP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2913
Polymers38,2562
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-43.6 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.410, 77.050, 403.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
VP16


Mass: 19127.773 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS PHAGE P23-77 (virus) / Plasmid: PIR2 (ORF16/PET22B) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: C8CHL4
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.5 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: SITTING DROP VAPOUR DIFFUSION SYSTEM, MICROLITER DROPS OF PURIFIED P23-77 VIRION (PROTEIN CONCENTRATION 2.4 MG/ML, SAMPLE BUFFER 20 MM TRIS-HCL PH 7.5, 5 MM MGCL2 AND 150 MM NACL) MIXED 1:1 ...Details: SITTING DROP VAPOUR DIFFUSION SYSTEM, MICROLITER DROPS OF PURIFIED P23-77 VIRION (PROTEIN CONCENTRATION 2.4 MG/ML, SAMPLE BUFFER 20 MM TRIS-HCL PH 7.5, 5 MM MGCL2 AND 150 MM NACL) MIXED 1:1 WITH SOLUTION CONSISTING OF 0.1 M CITRIC ACID PH 3.5, 20 MM TRIS-HCL PH 7.5, 5 MM MGCL2, 150 MM NACL AND 25%(W/V) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.36→42.16 Å / Num. obs: 54151 / % possible obs: 99.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 52.18 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.5
Reflection shellResolution: 2.36→2.42 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
xia2data reduction
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 3ZMO
Resolution: 2.36→42.16 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.9101 / SU R Cruickshank DPI: 0.449 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.472 / SU Rfree Blow DPI: 0.246 / SU Rfree Cruickshank DPI: 0.248
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. RESIDUES 1 AND 171- 173 ARE DISORDERED IN CHAIN A, RESIDUES 1 AND 170-173 ARE DISORDERED IN CHAIN B, ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. RESIDUES 1 AND 171- 173 ARE DISORDERED IN CHAIN A, RESIDUES 1 AND 170-173 ARE DISORDERED IN CHAIN B, RESIDUES 1 AND 169-173 ARE DISORDERED IN CHAINS C AND F, RESIDUES 1, 124- -129 AND 169-173 ARE DISORDERED IN CHAIN D, RESIDUES 1 AND 168-173 ARE DISORDERED IN CHAIN E, RESIDUES 1-3 AND 169- -173 ARE DISORDERED IN CHAIN G, RESIDUES 1, 123-127 AND 169-173 ARE DISORDERED IN CHAIN H.
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 2743 5.08 %RANDOM
Rwork0.1925 ---
obs0.1946 53974 98.59 %-
Displacement parametersBiso mean: 52.25 Å2
Baniso -1Baniso -2Baniso -3
1--10.2165 Å20 Å20 Å2
2---0.8751 Å20 Å2
3---11.0916 Å2
Refine analyzeLuzzati coordinate error obs: 0.308 Å
Refinement stepCycle: LAST / Resolution: 2.36→42.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10375 0 4 348 10727
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110632HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0714517HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3545SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes259HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1538HARMONIC5
X-RAY DIFFRACTIONt_it10632HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion16.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1356SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11421SEMIHARMONIC4
LS refinement shellResolution: 2.36→2.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2862 224 5.72 %
Rwork0.2286 3691 -
all0.2318 3915 -
obs--98.59 %
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)
10.2813-0.3248-0.05830.25750.45750.0346-0.0020.0124-0.00370.00070.00180.00810.00370.01780.00020.02590.0880.0279-0.0213-0.0901-0.001927.0264-10.5281-121.672
20.92840.0774-0.65560.4887-0.22032.21620.02020.0247-0.0231-0.1497-0.00810.02650.0205-0.0778-0.0121-0.08290.0089-0.0313-0.1087-0.01580.04195.2730.7999-98.729
30.6404-0.2764-1.06061.0112-0.05171.0401-0.0016-0.0201-0.046-0.00540.0440.08980.0339-0.0117-0.0423-0.1108-0.0261-0.0343-0.01910.00940.0515-1.4554-3.6334-89.8306
40-0.2318-0.43180.09640.21670.01780.00160.0117-0.0071-0.0187-0.0003-0.00340.0265-0.0033-0.00140.0438-0.0454-0.034-0.0288-0.02040.01774.5866-14.2742-95.9037
50.8716-0.0911-0.31190.00010.04691.44620.0168-0.00270.01440.0237-0.01510.0158-0.08170.019-0.0017-0.04290.0336-0.0454-0.0483-0.01680.02025.4408-0.9713-86.2442
60.1960.07580.05890.0741-0.27880.0140.00350.006500.00850.01470.00770.00670.0122-0.0182-0.0359-0.05070.022-0.0020.02250.03281.6034-17.5731-79.0624
70.65120.0816-0.52890.0065-0.05753.17880.01930.01-0.0086-0.05260.0166-0.0122-0.03270.0493-0.0359-0.02130.026-0.0161-0.11620.00480.016814.34533.0205-102.227
80.3891-0.1794-1.17360.0154-0.75431.89720.01110.0375-0.0177-0.04360.0389-0.01090.02190.1171-0.05-0.01160.008-0.0081-0.0112-0.0167-0.015823.38062.968-110.884
90.091-0.7017-0.04230-0.64370.0031-0.0021-0.00610.01150.0051-0.0139-0.00480.0073-0.00280.01590.01360.02840.0020.00610.0607-0.002321.8081-10.9867-103.592
100.76190.54210.12960-0.08042.88820.00510.0567-0.0018-0.0235-0.02340.00410.0329-0.04280.0183-0.00450.0282-0.0271-0.0515-0.0123-0.000315.41032.0148-114.203
110.0811-0.0338-0.050800.0660.2244-0.0009-0.0150.0013-0.0038-0.002-0.0106-0.0007-0.01020.0030.02380.02290.01540.00580.0228-0.037-1.927613.617419.2733
120.00270.2945-0.27940.56840.37791.16540.0063-0.0479-0.04060.0898-0.00430.0035-0.00810.062-0.0020.01730.0433-0.0129-0.00760.0214-0.04718.9017-5.0259-2.0217
130.8581-0.23520.22140.0089-0.13782.10380.01250.0557-0.07030.01770.0421-0.00880.0162-0.0155-0.05460.0087-0.0020.0079-0.01860.0079-0.024817.4259-11.3669-7.214
140.57921.2183-0.33040.36820.32370.02570.0052-0.0239-0.01420.00020.001-0.0030.03480.0024-0.00610.00760.01510.0151-0.03940.00010.012311.0037-18.3398-6.1798
150.4928-0.55060.82941.8677-0.28621.9091-0.00090.03980.00670.02070.04920.0308-0.07930.0152-0.04830.04850.02830.016-0.04520.0295-0.057516.1238-7.7488-10.9992
160.17140.37840.26460.02910.1940.3737-0.00040.0194-0.0125-0.0097-0.00390.0125-0.0025-0.01650.0042-0.00650.0068-0.03160.03-0.017-0.02032.3681-16.7002-19.3179
170.38730.14330.13120.90561.32892.18860.02240.05620.03710.02420.0250.0455-0.036-0.0109-0.04740.10030.0242-0.0132-0.09340.0446-0.054216.58537.51724.0095
180.01990.1176-0.00250.05510.020400.0002-0.00210.00850.005-0.00170.0044-0.0056-0.00720.0015-0.0040.01590.0129-0.0157-0.00390.039811.822227.541613.206
190.75220.40610.01260.01620.75131.9275-0.00430.0052-0.0010.01970.03930.001-0.0143-0.044-0.0350.03210.0181-0.0005-0.05630.0303-0.024714.93139.60929.3162
200.0016-0.4706-0.37120.4530.20010.25730.001-0.0087-0.0022-0.0054-0.00810.007-0.0003-0.01750.00710.0313-0.02070.0547-0.0266-0.0106-0.01647.16329.440219.539
210.03650.0146-0.30520.28240.00190-0.00040.01140.0062-0.00080.0003-0.0009-0.00520.00450.00010.0245-0.01210.0376-0.05680.0290.02958.308317-69.1617
220.7402-0.08670.37210-0.41483.82170.0085-0.03660.04190.01870.05610.02730.13720.103-0.06460.0698-0.0289-0.0085-0.0684-0.0322-0.069214.8222-8.1101-48.267
230.0004-0.79450.74350.0105-0.41721.36910.0001-0.0048-0.0117-0.0010.0035-0.0084-0.02350.0144-0.00360.0667-0.0019-0.0090.0158-0.0451-0.097214.7941-0.1768-43.9888
240.4148-0.2675-0.74740.1084-0.00531.0671-0.00550.0365-0.0057-0.0190.0206-0.01810.02340.0434-0.01510.04250.1193-0.01790.08360.0023-0.115728.8635-13.9745-39.7101
250.1894-0.08030.10311.4726-0.41154.73050.0079-0.00440.0109-0.0260.03380.01020.0690.0474-0.04170.10890.0039-0.0214-0.0094-0.0084-0.130317.9658-7.8087-37.6506
260.1045-0.02260.026500.10010.1941-0.00120.00070.00640.0011-0.00230.0025-0.00020.0090.00350.00510.0015-0.0120.0360.0131-0.038532.7838-0.0822-29.6508
270.4188-0.30760.71660.1509-0.4042.39720.0091-0.0692-0.02630.08840.03040.02190.067-0.0422-0.03950.016-0.02420.0027-0.0463-0.0006-0.03955.6848-0.838-52.9037
280.0040.1973-0.06331.48360.50050.43950.005-0.00430.0230.021-0.00340.0193-0.0189-0.0095-0.00170.0228-0.0035-0.0253-0.0263-0.02490.01420.741312.0983-58.2205
290.2929-1.22420.65041.6577-1.02451.6179-0.0062-0.0555-0.01130.00780.02080.01720.07220.0054-0.0147-0.0225-0.08480.0008-0.0047-0.0352-0.05855.4791-0.1906-59.7846
300.0537-0.17140.15190.179-0.37640.1476-0.00010.0027-0.00310.00070.0074-0.0002-0.00540.0069-0.00730.0054-0.00620.02090.00550.031-0.007812.96448.7248-72.0822
310.1730.0269-0.01430.0583-0.01940.22020.00110.00050.00250.0015-0.0039-0.0038-0.00410.00830.00270.0301-0.0003-0.00410.04870.02380.012752.809233.3238-31.2208
320-0.11290.07020.4493-0.09832.39070.0167-0.0697-0.00650.0796-0.05-0.03430.0295-0.06340.03330.0236-0.0653-0.0066-0.05470.0207-0.019126.763438.109-51.8537
330.0005-0.30350.130.2389-0.46692.11790.0027-0.00160.04390.0216-0.0140.04710.03830.06660.01130.07840.00910.0076-0.0177-0.0182-0.071530.944740.1256-55.5679
340.1991-0.40770.27110.3465-0.07850.1215-0.0011-0.00480.0103-0.00130.0004-0.0031-0.0018-0.00650.00060.04080.0134-0.0137-0.03130.0229-0.007116.129354.6795-64.4414
3500.27360.59370.63930.41560.24920.006-0.01710.01220.0169-0.0069-0.011-0.021-0.00440.00080.0614-0.0391-0.0142-0.0136-0.0168-0.045232.531852.037-56.6927
360.07760.0059-0.22910.4483-0.27523.16620.00140.03290.0040.0488-0.01410.01050.0524-0.00080.01270.0209-0.0408-0.0112-0.0211-0.0009-0.061127.473240.5349-62.7422
370.45990.5618-0.12090-0.21811.8459-0.00250.00870.01610.00840.00440.0029-0.01430.0119-0.00190.0453-0.10110.0129-0.04530.013-0.018434.096249.1629-71.8211
380.3770.00580.3420.5368-0.824.0551-0.0125-0.07710.0546-0.02310.01110.00740.11910.02950.00130.0867-0.0405-0.0121-0.05550.0417-0.056832.190726.8543-42.9735
390.1955-0.184-0.03441.0120.29283.0171-0.0124-0.0085-0.0615-0.0140.0006-0.00850.06520.07560.01190.10060.01670.03660.0142-0.0095-0.069237.75924.0871-41.4945
400.0654-0.2312-0.59080.11850.22170.3592-0.00250.00710.014-0.00170.0035-0.009-0.00440.0051-0.0010.01340.02920.05150.0420.0155-0.032546.096927.0994-43.9368
410.00531.5574-0.85132.0684-2.1512.7278-0.0166-0.04980.0099-0.0080.02460.01750.0610.0166-0.0080.0954-0.0403-0.0343-0.01980.0298-0.110233.263428.6155-36.8773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|2 - A|12 }
2X-RAY DIFFRACTION2{ A|13 - A|77 }
3X-RAY DIFFRACTION3{ A|78 - A|115 }
4X-RAY DIFFRACTION4{ A|116 - A|127 }
5X-RAY DIFFRACTION5{ A|128 - A|170 }
6X-RAY DIFFRACTION6{ B|2 - B|12 }
7X-RAY DIFFRACTION7{ B|13 - B|79 }
8X-RAY DIFFRACTION8{ B|80 - B|117 }
9X-RAY DIFFRACTION9{ B|118 - B|127 }
10X-RAY DIFFRACTION10{ B|128 - B|169 }
11X-RAY DIFFRACTION11{ C|2 - C|16 }
12X-RAY DIFFRACTION12{ C|17 - C|79 }
13X-RAY DIFFRACTION13{ C|80 - C|108 }
14X-RAY DIFFRACTION14{ C|109 - C|124 }
15X-RAY DIFFRACTION15{ C|125 - C|168 }
16X-RAY DIFFRACTION16{ D|2 - D|16 }
17X-RAY DIFFRACTION17{ D|17 - D|105 }
18X-RAY DIFFRACTION18{ D|106 - D|111 }
19X-RAY DIFFRACTION19{ D|112 - D|159 }
20X-RAY DIFFRACTION20{ D|160 - D|168 }
21X-RAY DIFFRACTION21{ E|2 - E|12 }
22X-RAY DIFFRACTION22{ E|13 - E|77 }
23X-RAY DIFFRACTION23{ E|78 - E|94 }
24X-RAY DIFFRACTION24{ E|95 - E|124 }
25X-RAY DIFFRACTION25{ E|125 - E|167 }
26X-RAY DIFFRACTION26{ F|2 - F|12 }
27X-RAY DIFFRACTION27{ F|13 - F|107 }
28X-RAY DIFFRACTION28{ F|108 - F|123 }
29X-RAY DIFFRACTION29{ F|124 - F|162 }
30X-RAY DIFFRACTION30{ F|163 - F|168 }
31X-RAY DIFFRACTION31{ G|4 - G|15 }
32X-RAY DIFFRACTION32{ G|16 - G|73 }
33X-RAY DIFFRACTION33{ G|74 - G|98 }
34X-RAY DIFFRACTION34{ G|99 - G|110 }
35X-RAY DIFFRACTION35{ G|111 - G|126 }
36X-RAY DIFFRACTION36{ G|127 - G|168 }
37X-RAY DIFFRACTION37{ H|2 - H|25 }
38X-RAY DIFFRACTION38{ H|26 - H|72 }
39X-RAY DIFFRACTION39{ H|73 - H|113 }
40X-RAY DIFFRACTION40{ H|114 - H|129 }
41X-RAY DIFFRACTION41{ H|130 - H|168 }

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