[English] 日本語
Yorodumi
- PDB-5mlf: Structure of Psb29 at 1.55A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mlf
TitleStructure of Psb29 at 1.55A
ComponentsProtein Thf1
KeywordsPHOTOSYNTHESIS / photosystem II FtsH
Function / homologyProtein Thf1 / Thylakoid formation protein / photosystem II assembly / : / Protein Thf1
Function and homology information
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.637 Å
AuthorsMurray, J.W. / Kozlo, A.
CitationJournal: Philos. Trans. R. Soc. Lond., B, Biol. Sci. / Year: 2017
Title: Structure of Psb29/Thf1 and its association with the FtsH protease complex involved in photosystem II repair in cyanobacteria.
Authors: Bec Kova, M. / Yu, J. / Krynicka, V. / Kozlo, A. / Shao, S. / Konik, P. / Komenda, J. / Murray, J.W. / Nixon, P.J.
History
DepositionDec 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein Thf1
B: Protein Thf1
C: Protein Thf1
D: Protein Thf1
E: Protein Thf1
G: Protein Thf1
F: Protein Thf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,28614
Polymers190,8827
Non-polymers1,4047
Water0
1
A: Protein Thf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4692
Polymers27,2691
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein Thf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4692
Polymers27,2691
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein Thf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4692
Polymers27,2691
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein Thf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4692
Polymers27,2691
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Protein Thf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4692
Polymers27,2691
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
G: Protein Thf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4692
Polymers27,2691
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
F: Protein Thf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4692
Polymers27,2691
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.910, 138.910, 305.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein
Protein Thf1 / psb29


Mass: 27268.848 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: thf1, tlr1134 / Plasmid: pRSETA modified / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q8DJT8
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Hg

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.97 % / Description: long thin rods
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 16% w/v PEG 6K, 80mM Na citrate pH 5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.637→55.98 Å / Num. obs: 20447 / % possible obs: 99.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.64 % / Rmerge(I) obs: 0.394 / Net I/av σ(I): 7.3697 / Net I/σ(I): 1.8947
Reflection shellResolution: 3.637→3.73 Å / Redundancy: 14.51 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.01 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MJR
Resolution: 3.637→55.977 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3575 1045 5.13 %
Rwork0.311 --
obs0.3134 20386 99.83 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.637→55.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11200 0 7 0 11207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211529
X-RAY DIFFRACTIONf_angle_d0.47115694
X-RAY DIFFRACTIONf_dihedral_angle_d11.6787021
X-RAY DIFFRACTIONf_chiral_restr0.0331757
X-RAY DIFFRACTIONf_plane_restr0.0032079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6375-3.82920.40121610.35692678X-RAY DIFFRACTION100
3.8292-4.06910.43991420.35482691X-RAY DIFFRACTION100
4.0691-4.38310.39671240.33062746X-RAY DIFFRACTION100
4.3831-4.8240.32261680.3072699X-RAY DIFFRACTION100
4.824-5.52150.37981550.32842747X-RAY DIFFRACTION100
5.5215-6.95440.37831290.30112822X-RAY DIFFRACTION100
6.9544-55.98360.26791660.24082958X-RAY DIFFRACTION99
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)
10.17260.0267-0.04980.0047-0.01430.03730.1665-0.2938-0.08520.1061-0.0387-0.06140.0780.04940.13651.0295-0.33210.38940.49960.10050.830129.3408-24.271770.2196
20.04810.06990.01380.06260.01480.14140.1772-0.1170.14660.06380.037-0.1496-0.25510.11720.25050.7724-0.34670.2338-0.2472-0.54750.566736.8953-29.455561.0837
30.00530.00250.02710.00460.02250.09430.0637-0.05890.0985-0.00080.03670.3222-0.03620.06690.02781.3963-0.58910.23110.72280.05291.028533.4025-18.98161.9842
40.06310.0497-0.02330.1303-0.05230.04770.0066-0.1351-0.00550.2112-0.13770.0412-0.02330.0738-0.23550.2339-0.1488-0.04620.19280.07990.38751.0622-28.867151.0113
50.0689-0.05080.12230.1225-0.26550.43590.0929-0.0025-0.19060.33220.25010.6547-0.4925-0.3704-0.1383-0.5201-0.24180.66940.15740.2544-0.149334.5035-35.605148.084
60.23790.2663-0.31960.2862-0.35840.4510.31330.2956-0.3675-0.01220.18680.33760.08990.0370.14040.9699-0.2526-0.57891.47890.57771.269417.0772-34.661617.0832
70.24390.02290.0340.12890.03630.0093-0.09450.04380.3125-0.09650.08570.108-0.08020.00380.11030.65170.4645-0.38820.97210.35480.437423.5591-40.323821.5734
80.21890.03220.37680.0090.03960.69960.1108-0.12660.2807-0.12040.57380.04410.20690.03220.12940.5156-0.02430.1940.97020.01670.67818.9574-44.52928.9549
90.07960.0604-0.13430.0505-0.10860.24630.1915-0.19280.18750.11440.30650.0022-0.0779-0.03270.04060.26140.2051-0.0411.07890.12780.776411.0364-37.558325.2605
100.2356-0.0311-0.20320.08120.09390.2513-0.02620.65450.1912-0.23680.29180.227-0.0912-0.34780.24060.5813-0.60980.30821.07760.09940.448615.067-54.697538.0543
110.0005-0.006-0.01520.03750.03540.0416-0.02790.0143-0.11950.10480.04510.11670.2181-0.133-0.03680.15980.3702-0.33870.4695-0.13180.131821.3621-60.53533.4008
120.4783-0.05910.0420.23860.08910.39240.107-0.1470.5160.0947-0.3599-0.00680.038-0.5171-0.8390.23880.01730.15820.6614-0.18620.156727.0097-41.741139.3336
130.04860.08010.00890.12140.02010.0281-0.03330.0234-0.0064-0.1048-0.08880.210.17970.01560.00120.9216-0.4059-0.24040.97710.54051.141933.189-27.1637-9.5212
140.0065-0.01680.00390.0549-0.01180.00270.1599-0.0896-0.0565-0.1135-0.00190.0178-0.00080.00870.04850.562-0.00990.16050.3970.32420.56326.1003-18.14091.4685
150.0602-0.0502-0.0610.06770.02930.1424-0.0314-0.03130.2476-0.05960.01570.1805-0.0856-0.03180.11120.114-0.3444-0.24460.5118-0.07030.637438.5017-25.7259-0.3982
160.03970.06840.04460.12720.07560.0488-0.0494-0.0739-0.00910.03520.09260.0628-0.048-0.0155-0.08681.14-0.0948-0.01120.59480.40440.69643.9227-39.8841-1.048
170.07440.023-0.05640.05550.01870.07480.1201-0.02750.1036-0.05930.11880.0043-0.0486-0.08110.182-0.2027-0.3115-0.24580.38240.22521.014832.622-27.800510.5009
180.05090.0698-0.04260.1135-0.07410.04610.0098-0.0080.1286-0.06580.11410.17290.0149-0.06890.20260.5321-0.6003-0.07520.84090.44420.316525.9826-28.66263.1728
190.08640.03910.01270.15470.01630.07720.0582-0.0566-0.2069-0.21990.2454-0.050.0951-0.01180.0938-0.16890.03370.30350.0367-0.12050.29239.7607-43.226614.4438
200.1995-0.0640.11220.1286-0.21580.3001-0.12620.094-0.1875-0.0756-0.01710.11430.07660.0701-0.1061-0.25540.68930.45660.0555-0.1415-0.08542.5699-33.019120.1252
210.074-0.0610.02280.0526-0.02170.085-0.08610.03510.148-0.2121-0.0188-0.14730.17430.01120.02930.2493-0.0199-0.00030.66360.19920.397752.5427-36.895219.3134
220.70620.0401-0.13070.4929-0.35160.68530.22130.20150.28050.1250.33720.28050.04790.04590.850.22390.3057-0.04660.4014-0.09670.055937.5239-16.41314.958
230.27-0.06450.04980.36180.6721.34460.2312-0.1850.13270.16420.418-0.14590.1657-0.07450.17550.9277-0.25790.66380.39190.02451.372636.6954-8.693348.5052
240.02390.0237-0.02360.11150.0860.1754-0.030.00690.06140.0165-0.19490.2095-0.23480.1037-0.41830.64490.05460.09140.4721-0.51220.272148.8051-12.10744.4098
250.22920.03070.05510.3328-0.17480.10550.10710.0137-0.0290.16430.19150.27690.035-0.02890.36430.3953-0.4020.3785-0.2776-0.03380.460141.8714-7.990833.1111
260.0129-0.03330.00220.1144-0.03840.06520.11450.0681-0.0924-0.01160.02540.1988-0.022-0.01260.04820.95590.5520.51010.81960.12591.102438.2592-2.163240.3047
270.010.0055-0.01110.0034-0.01330.13690.0855-0.1154-0.05360.11250.1487-0.0250.0314-0.00640.33610.68990.11580.40380.1478-0.47180.581351.11890.440933.8028
280.1293-0.03740.11480.001-0.01210.11030.1008-0.0816-0.20610.2190.06480.0830.05290.06530.4266-0.12330.2102-0.35360.00460.03570.491763.0369-6.658326.6427
290.07720.07790.05660.3541-0.19380.182-0.1984-0.4012-0.22360.4518-0.0453-0.126-0.2955-0.2493-0.7053-0.20850.628-0.3484-0.48220.47670.063646.1035-16.845326.4265
300.2946-0.10370.32990.301-0.05620.3834-0.2246-0.03150.00430.0185-0.11730.0477-0.055-0.1558-0.28920.9212-0.42010.37290.7282-0.53860.587919.0722-38.038296.7442
31-0.0016-0.005-0.0119-0.0022-0.0023-0.0031-0.1138-0.12260.0639-0.00120.02360.0699-0.0015-0.1425-0.18720.6722-0.06320.81390.6874-0.39020.642314.7694-38.007586.8907
320.10890.0123-0.08290.43080.39050.56440.07250.07770.30720.15110.36580.28540.0380.01010.60410.5109-0.31220.41130.3233-0.07960.538922.8005-42.134680.3643
33-0.03070.0115-0.02970.0306-0.0058-0.01520.4829-0.33950.17910.3247-0.20350.1253-0.46580.35020.92520.6233-0.22140.38760.3537-0.04790.03830.7838-44.197675.6414
340.2561-0.0540.01640.1502-0.00730.05190.1190.16230.25540.09040.08710.14080.0183-0.06670.13720.5924-0.12790.05120.15470.00920.287523.0035-49.100167.3373
350.1440.0974-0.09690.0774-0.05350.11140.04550.02540.0550.04790.04370.0422-0.0423-0.01040.19390.57510.12780.75210.44950.34060.976324.7925-59.588868.4058
360.06780.09560.07670.14960.02280.27340.08510.0230.06090.08080.03330.0644-0.28080.0849-0.04030.3908-0.0150.14030.19460.18390.80537.7442-40.677672.2908
370.1510.07870.03660.042-0.02830.23370.28080.13710.2081-0.10870.1506-0.0260.2034-0.1150.64010.05460.51010.03460.51290.27170.79940.9032-44.963641.1246
380.2043-0.0586-0.110.02560.03010.07940.11890.11960.1925-0.0745-0.0834-0.1346-0.1886-0.2676-0.07830.5980.19280.23930.8760.3730.893-1.2598-43.220154.411
3900.0024-0.00090.0053-0.01260.03760.0307-0.11450.08840.0116-0.0034-0.01260.0185-0.02040.09460.70710.52220.37971.16210.05941.131-6.043-38.41547.1435
400.0006-0.0112-0.00840.0176-0.0037-0.0016-0.12710.35370.0969-0.0673-0.05430.07870.00450.1134-0.30470.4170.22470.38970.90570.7540.3673-11.6357-50.166153.7881
410.5567-0.6135-0.19860.91070.52960.73120.44010.07820.1391-0.47050.5008-0.1958-0.0237-0.39662.05690.156-0.04360.21270.54010.19880.20762.2648-53.468561.1815
420.00460.01790.01060.04450.03360.0276-0.07340.07660.0048-0.0314-0.06330.0579-0.03310.0344-0.16371.0523-0.6737-0.48270.47890.14780.592741.8841-10.3586-31.2021
430.03590.00840.03720.00440.00940.04010.15950.066-0.0334-0.0454-0.026-0.00760.00850.06690.01950.65960.04790.03450.2096-0.25180.490531.764-5.095-20.1682
440.0333-0.0137-0.01220.0892-0.0560.09980.11790.04210.0623-0.1084-0.02310.39440.1147-0.07610.04440.6494-0.2615-0.34870.0821-0.01890.752446.1842-6.7298-22.1369
450.16020.1072-0.00940.1782-0.0190.1154-0.05330.04060.0766-0.2490.1088-0.02620.14030.00980.10890.5832-0.61470.51710.2444-0.02160.107646.5332-12.9271-14.7357
460.021-0.03720.00790.19530.10830.1130.1198-0.01260.07960.02180.120.1256-0.1137-0.01760.21651.1211-0.6003-0.30490.7690.56971.025136.1261-14.6541-18.4177
470.0320.04260.04520.16820.00820.1233-0.00490.0093-0.1157-0.0808-0.0161-0.1501-0.133-0.02110.16190.991-1.017-0.12380.85380.41590.501346.3712-22.6445-11.7314
48-0.0003-0.00420.00770.0736-0.10990.166-0.0117-0.0271-0.00450.1081-0.1008-0.00060.02980.0182-0.14911.0717-0.06630.36280.24820.07010.010259.7794-21.94223.0355
490.4736-0.1902-0.42630.15140.25830.50080.21040.08770.2132-0.25580.0693-0.1418-0.33860.17180.2610.1816-0.16050.37640.3999-0.17330.047356.9612-17.2202-8.3924
500.00130.0261-0.01490.0818-0.04570.0226-0.0776-0.04510.1973-0.1871-0.0416-0.03040.0799-0.066-0.10180.1982-0.3406-0.04890.23590.78930.073260.2171-10.47660.4339
510.01980.0045-0.07620.0064-0.07930.16250.0233-0.27260.11480.0503-0.12290.12990.2243-0.00450.122-0.15710.01070.24010.0125-0.24860.161941.50121.4295-6.8087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 69 )
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 132 )
5X-RAY DIFFRACTION5chain 'A' and (resid 133 through 206 )
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 26 )
7X-RAY DIFFRACTION7chain 'B' and (resid 27 through 41 )
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 69 )
9X-RAY DIFFRACTION9chain 'B' and (resid 70 through 84 )
10X-RAY DIFFRACTION10chain 'B' and (resid 85 through 114 )
11X-RAY DIFFRACTION11chain 'B' and (resid 115 through 132 )
12X-RAY DIFFRACTION12chain 'B' and (resid 133 through 206 )
13X-RAY DIFFRACTION13chain 'C' and (resid 4 through 17 )
14X-RAY DIFFRACTION14chain 'C' and (resid 18 through 26 )
15X-RAY DIFFRACTION15chain 'C' and (resid 27 through 41 )
16X-RAY DIFFRACTION16chain 'C' and (resid 42 through 49 )
17X-RAY DIFFRACTION17chain 'C' and (resid 50 through 69 )
18X-RAY DIFFRACTION18chain 'C' and (resid 70 through 84 )
19X-RAY DIFFRACTION19chain 'C' and (resid 85 through 132 )
20X-RAY DIFFRACTION20chain 'C' and (resid 133 through 153 )
21X-RAY DIFFRACTION21chain 'C' and (resid 154 through 168 )
22X-RAY DIFFRACTION22chain 'C' and (resid 169 through 206 )
23X-RAY DIFFRACTION23chain 'D' and (resid 4 through 26 )
24X-RAY DIFFRACTION24chain 'D' and (resid 27 through 49 )
25X-RAY DIFFRACTION25chain 'D' and (resid 50 through 69 )
26X-RAY DIFFRACTION26chain 'D' and (resid 70 through 84 )
27X-RAY DIFFRACTION27chain 'D' and (resid 85 through 101 )
28X-RAY DIFFRACTION28chain 'D' and (resid 102 through 132 )
29X-RAY DIFFRACTION29chain 'D' and (resid 133 through 206 )
30X-RAY DIFFRACTION30chain 'E' and (resid 4 through 17 )
31X-RAY DIFFRACTION31chain 'E' and (resid 18 through 41 )
32X-RAY DIFFRACTION32chain 'E' and (resid 42 through 69 )
33X-RAY DIFFRACTION33chain 'E' and (resid 70 through 132 )
34X-RAY DIFFRACTION34chain 'E' and (resid 133 through 153 )
35X-RAY DIFFRACTION35chain 'E' and (resid 154 through 168 )
36X-RAY DIFFRACTION36chain 'E' and (resid 169 through 206 )
37X-RAY DIFFRACTION37chain 'G' and (resid 4 through 49 )
38X-RAY DIFFRACTION38chain 'G' and (resid 50 through 69 )
39X-RAY DIFFRACTION39chain 'G' and (resid 70 through 84 )
40X-RAY DIFFRACTION40chain 'G' and (resid 85 through 101 )
41X-RAY DIFFRACTION41chain 'G' and (resid 102 through 206 )
42X-RAY DIFFRACTION42chain 'F' and (resid 4 through 17 )
43X-RAY DIFFRACTION43chain 'F' and (resid 18 through 26 )
44X-RAY DIFFRACTION44chain 'F' and (resid 27 through 41 )
45X-RAY DIFFRACTION45chain 'F' and (resid 42 through 69 )
46X-RAY DIFFRACTION46chain 'F' and (resid 70 through 84 )
47X-RAY DIFFRACTION47chain 'F' and (resid 85 through 101 )
48X-RAY DIFFRACTION48chain 'F' and (resid 102 through 114 )
49X-RAY DIFFRACTION49chain 'F' and (resid 115 through 145 )
50X-RAY DIFFRACTION50chain 'F' and (resid 146 through 168 )
51X-RAY DIFFRACTION51chain 'F' and (resid 169 through 206 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more