[English] 日本語
Yorodumi
- PDB-5ol5: Crystal structure of an inactivated Ssp SICLOPPS intein with CFAH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ol5
TitleCrystal structure of an inactivated Ssp SICLOPPS intein with CFAHPQ extein
Components(DNA polymerase III subunit alpha,DNA polymerase III subunit ...) x 2
KeywordsSPLICING / intein / extein / SICLOPPS / cyclic peptide
Function / homology
Function and homology information


intein-mediated protein splicing / 3'-5' exonuclease activity / DNA-directed DNA polymerase / nucleic acid binding / DNA-directed DNA polymerase activity / DNA replication / cytoplasm
Similarity search - Function
Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / PHP domain / PHP domain ...Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain
Similarity search - Domain/homology
: / DNA polymerase III subunit alpha
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.329 Å
AuthorsKick, L.M. / Schneider, S.
Funding support Germany, 4items
OrganizationGrant numberCountry
Center for Integrated Protein Science Germany
German Research FoundationSCHN1273 Germany
German Research FoundationSFB749 Germany
Fonds der chemischen Industrie Germany
CitationJournal: Chembiochem / Year: 2017
Title: Mechanistic Insights into Cyclic Peptide Generation by DnaE Split-Inteins through Quantitative and Structural Investigation.
Authors: Kick, L.M. / Harteis, S. / Koch, M.F. / Schneider, S.
History
DepositionJul 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.5Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase III subunit alpha,DNA polymerase III subunit alpha
B: DNA polymerase III subunit alpha,DNA polymerase III subunit alpha
C: DNA polymerase III subunit alpha,DNA polymerase III subunit alpha
D: DNA polymerase III subunit alpha,DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9809
Polymers77,5434
Non-polymers4365
Water2,252125
1
A: DNA polymerase III subunit alpha,DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6473
Polymers19,3941
Non-polymers2532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA polymerase III subunit alpha,DNA polymerase III subunit alpha


Theoretical massNumber of molelcules
Total (without water)19,3941
Polymers19,3941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA polymerase III subunit alpha,DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5023
Polymers19,3781
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA polymerase III subunit alpha,DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4372
Polymers19,3781
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.120, 92.129, 110.448
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

-
DNA polymerase III subunit alpha,DNA polymerase III subunit ... , 2 types, 4 molecules ABCD

#1: Protein DNA polymerase III subunit alpha,DNA polymerase III subunit alpha


Mass: 19393.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria), (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: dnaE-N, slr0603, dnaE-C, sll1572 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P74750, DNA-directed DNA polymerase
#2: Protein DNA polymerase III subunit alpha,DNA polymerase III subunit alpha


Mass: 19377.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria), (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: dnaE-N, slr0603, dnaE-C, sll1572 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P74750, DNA-directed DNA polymerase

-
Non-polymers , 4 types, 130 molecules

#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50mM Tris-HCl pH 8.0, 200mM MgCl2, 25%(w/v) PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.329→55.224 Å / Num. obs: 26852 / % possible obs: 98.3 % / Redundancy: 14 % / CC1/2: 0.998 / Rmerge(I) obs: 0.189 / Net I/σ(I): 8.1
Reflection shellResolution: 2.33→2.4 Å / Redundancy: 13.1 % / Num. unique obs: 2579 / CC1/2: 0.7 / % possible all: 93.4

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OL1

5ol1


Resolution: 2.329→55.224 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.47
RfactorNum. reflection% reflection
Rfree0.2759 1311 4.95 %
Rwork0.2309 --
obs0.2331 26472 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.329→55.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 17 125 4560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054557
X-RAY DIFFRACTIONf_angle_d0.6076181
X-RAY DIFFRACTIONf_dihedral_angle_d11.7763191
X-RAY DIFFRACTIONf_chiral_restr0.043703
X-RAY DIFFRACTIONf_plane_restr0.004810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3293-2.42260.41011370.3812599X-RAY DIFFRACTION94
2.4226-2.53280.37541440.35252720X-RAY DIFFRACTION97
2.5328-2.66640.37541280.33242760X-RAY DIFFRACTION98
2.6664-2.83340.30381500.29962774X-RAY DIFFRACTION99
2.8334-3.05220.35861450.28262783X-RAY DIFFRACTION99
3.0522-3.35930.30241580.23552805X-RAY DIFFRACTION99
3.3593-3.84530.26221550.21532831X-RAY DIFFRACTION100
3.8453-4.84420.19551420.1662886X-RAY DIFFRACTION100
4.8442-55.23950.24691520.19333003X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.05141.3625-0.67848.2662-3.4077.4826-0.4258-0.31080.19231.21580.25270.1750.5730.2252-0.0470.837-0.0591-0.03340.388-0.01070.2873-0.667623.4793-17.6008
22.05641.5703-1.02145.5765-4.84694.4588-0.2465-0.17790.26670.7678-0.0344-0.1739-1.245-0.15670.7560.3296-0.00050.00210.286-0.03160.3497-3.838636.6013-5.4606
31.1197-0.87380.49445.0994-0.4248.95250.0878-0.30360.0799-0.06790.0808-0.02010.2602-0.0623-0.18250.3127-0.11910.01170.3805-0.03810.2872-3.411127.7841-0.1826
46.31235.03932.67624.09042.51852.48170.32110.34040.59070.4934-0.15251.42860.6802-1.12310.13350.40060.03730.03630.5152-0.03040.4319-12.62933.4509-0.0881
56.5266-2.299-5.45618.93383.37998.22690.15820.4975-0.09940.8602-0.85020.07110.9768-0.58710.49290.3775-0.1248-0.03690.4101-0.02290.3207-4.706422.55526.3122
61.4272-2.1213-0.46555.5269-1.97735.4765-0.0232-0.45880.29731.12340.3237-0.0599-0.19030.0787-0.16710.3284-0.1019-0.00550.4976-0.13110.3589-4.46529.44136.9185
75.52180.04090.10948.46751.85496.12770.16920.49820.2589-0.6293-0.39430.77330.416-0.27570.10120.4617-0.03240.04870.3757-0.01370.2427-3.031829.9124-13.1909
85.6528-0.11481.30747.95260.85285.8385-0.1231-0.673-0.3397-0.55050.0766-0.85470.90032.0672-0.21720.47620.2310.11910.55290.03420.43295.930523.1033-6.1884
93.40571.0776-0.81731.7571.87183.3648-0.9777-1.5589-0.0946-0.9219-0.5659-1.73350.61051.8185-0.44240.57760.44770.45090.7896-0.2125-0.09347.339524.515-12.4119
103.2705-3.01572.84163.8882-0.14488.18671.3191.0028-0.4103-0.69290.009-0.18351.80571.52720.17591.41930.17460.23560.54750.02360.32422.69316.6627-10.38
114.26112.0953-1.69643.4913-3.61224.7428-0.2511-0.3352-0.205-0.8754-0.0177-0.58490.2432-0.37940.23870.60340.1190.02810.5376-0.12420.393-30.167524.0122-5.1794
120.6731-0.37311.57535.34490.07497.5068-0.04620.10030.06020.2014-0.24510.36820.0844-0.68520.2870.28660.01410.0430.5785-0.13510.4869-31.450915.755-20.3583
134.86640.34160.47823.80480.18680.51340.1460.9562-0.1532-1.4208-0.14971.2847-0.3458-0.238-0.26680.76760.2661-0.0841.096-0.25920.9684-43.549721.238-24.7232
141.24762.4661-1.13435.0902-2.6346.192-0.3723-1.2853-0.9085-0.87320.56451.3110.1203-1.97860.34370.4734-0.14210.05291.1375-0.36930.7661-42.703813.184-22.361
152.02620.35230.35352.84790.59398.1952-0.11190.2198-0.0962-0.1509-0.22880.3975-0.0105-1.35370.47920.35050.12070.01180.5696-0.20290.5159-33.671219.2213-20.713
168.18261.68831.226.9367-2.2469.773-0.17980.18780.02980.08730.0887-0.6705-1.14820.35360.08340.4260.02770.00350.3811-0.04030.3531-24.321625.0246-13.5533
171.362-1.72881.72016.272-7.23558.33960.08840.0961-0.5094-0.77140.23780.60431.9364-0.588-0.14481.0097-0.00060.0540.4352-0.03340.4925-29.703513.07229.2314
187.3508-0.7165-1.97422.0796-1.79825.31080.1103-0.5161-0.1458-0.0007-0.2097-0.1119-0.05950.4004-0.06210.2827-0.01450.02240.21350.02360.2983-37.478835.457313.5621
195.8105-1.964-2.095.9545-0.32718.18040.09060.2648-0.1944-0.4536-0.26820.06890.05780.01160.19810.1927-0.0447-0.00650.2169-0.02070.2573-34.914636.23856.2921
207.20953.577-2.57335.1586-4.13595.69390.1776-0.19010.53370.23650.1624-0.2534-0.56760.8025-0.1970.2934-0.05-0.03780.19870.01040.3285-36.242742.958214.7053
214.3492-1.4491-4.4093.59712.75335.34810.2933-0.63480.0610.2387-0.1464-0.31860.12540.5215-0.06170.3611-0.0886-0.09490.30290.00940.4007-30.496941.869912.8283
221.09910.0198-0.17081.122-1.03691.1586-0.3646-0.3895-0.17810.89550.25080.51650.86910.0802-0.07471.27190.19870.29040.50750.13330.5918-26.839613.250916.725
232.34660.2357-3.14571.56252.10096.9335-0.3163-0.2383-0.1944-0.475-0.01650.65741.84851.21390.09721.43310.25410.11020.49720.08260.6285-23.95517.385221.4714
243.4575-0.39590.0762.6533-2.56893.56020.052-0.3225-0.1720.21710.083-0.41430.76830.60940.41390.50340.1191-0.04490.37720.01390.3629-0.898112.076422.9387
252.3249-0.9497-0.283.26780.53981.03170.14680.7204-0.0236-1.2881-0.3818-0.7488-0.2418-0.96420.20370.04690.1022-0.18990.4429-0.12510.40590.156337.827316.7324
262.82540.97923.73127.6663-1.45565.9567-0.1929-0.0319-0.2519-0.0177-0.2245-0.45140.4276-0.04050.29470.3921-0.01620.06120.25590.02290.351113.052332.771220.9071
275.76291.3127-2.82297.2462-3.52996.40920.093-0.14810.29430.82170.1443-0.00320.0667-0.0311-0.10890.24760.0144-0.02720.2564-0.01260.28625.45834.870824.5831
283.88583.2430.72245.5717-1.3742.05140.22-1.65210.63950.5362-0.17520.5277-0.5598-0.01540.07980.259-0.04390.05410.46610.0170.23363.501436.576530.2326
294.2497-1.7284-2.3823.88891.23348.7374-0.12370.2106-0.0149-0.0084-0.28540.06290.1418-0.07020.63260.22960.039-0.05030.2199-0.0050.39486.881443.05617.2462
303.06061.0861-3.16614.7587-0.24164.3640.00740.40331.0522-0.60290.07971.0423-0.0643-0.5845-0.13580.26620.0471-0.03310.2149-0.08580.47480.143141.250320.4044
316.6646-0.24581.23524.54660.28356.3383-0.0527-0.57760.3707-0.29540.4367-0.78121.21710.181-0.41140.5330.0225-0.03240.4263-0.12830.3607-2.197316.469722.3711
327.93081.18393.40951.91151.14946.3503-0.4340.3289-0.4138-0.79820.5795-0.17410.8271-0.04240.02021.0841-0.11250.11360.32580.05210.3731-4.462710.913111.3836
330.29410.84140.03195.1626-3.35794.774-0.53390.1996-0.5412-0.66340.26640.02281.7203-0.690.0151.0509-0.1530.01190.3430.04330.5348-6.64667.299610.274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 20 )
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 55 )
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 66 )
5X-RAY DIFFRACTION5chain 'A' and (resid 67 through 80 )
6X-RAY DIFFRACTION6chain 'A' and (resid 81 through 91 )
7X-RAY DIFFRACTION7chain 'A' and (resid 92 through 110 )
8X-RAY DIFFRACTION8chain 'A' and (resid 111 through 122 )
9X-RAY DIFFRACTION9chain 'A' and (resid 123 through 131 )
10X-RAY DIFFRACTION10chain 'A' and (resid 132 through 140 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 9 )
12X-RAY DIFFRACTION12chain 'B' and (resid 10 through 48 )
13X-RAY DIFFRACTION13chain 'B' and (resid 49 through 55 )
14X-RAY DIFFRACTION14chain 'B' and (resid 56 through 66 )
15X-RAY DIFFRACTION15chain 'B' and (resid 67 through 110 )
16X-RAY DIFFRACTION16chain 'B' and (resid 111 through 140 )
17X-RAY DIFFRACTION17chain 'C' and (resid 2 through 15 )
18X-RAY DIFFRACTION18chain 'C' and (resid 16 through 39 )
19X-RAY DIFFRACTION19chain 'C' and (resid 40 through 65 )
20X-RAY DIFFRACTION20chain 'C' and (resid 66 through 80 )
21X-RAY DIFFRACTION21chain 'C' and (resid 81 through 91 )
22X-RAY DIFFRACTION22chain 'C' and (resid 92 through 122 )
23X-RAY DIFFRACTION23chain 'C' and (resid 123 through 141 )
24X-RAY DIFFRACTION24chain 'D' and (resid 2 through 15 )
25X-RAY DIFFRACTION25chain 'D' and (resid 16 through 25 )
26X-RAY DIFFRACTION26chain 'D' and (resid 26 through 39 )
27X-RAY DIFFRACTION27chain 'D' and (resid 40 through 55 )
28X-RAY DIFFRACTION28chain 'D' and (resid 56 through 65 )
29X-RAY DIFFRACTION29chain 'D' and (resid 66 through 80 )
30X-RAY DIFFRACTION30chain 'D' and (resid 81 through 91 )
31X-RAY DIFFRACTION31chain 'D' and (resid 92 through 102 )
32X-RAY DIFFRACTION32chain 'D' and (resid 103 through 122 )
33X-RAY DIFFRACTION33chain 'D' and (resid 123 through 141 )

+
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