[English] 日本語
Yorodumi
- PDB-6wam: Structure of Acinetobacter baumannii Cap4 SAVED/CARF-domain conta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wam
TitleStructure of Acinetobacter baumannii Cap4 SAVED/CARF-domain containing receptor
ComponentsSAVED domain-containing protein
KeywordsHYDROLASE / nuclease / DUF4297 / SAVED / CARF / phage immunity
Function / homology
Function and homology information


defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
CD-NTase associated protein 4, DNA endonuclease domain / Cap4, dsDNA endonuclease domain / SMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain
Similarity search - Domain/homology
CD-NTase-associated protein 4
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLowey, B. / Whiteley, A.T. / Keszei, A.F.A. / Morehouse, B.R. / Antine, S.P. / Cabrera, V. / Schwede, F. / Mekalanos, J.J. / Shao, S. / Lee, A.S.Y. / Kranzusch, P.J.
CitationJournal: Cell / Year: 2020
Title: CBASS Immunity Uses CARF-Related Effectors to Sense 3'-5'- and 2'-5'-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection.
Authors: Lowey, B. / Whiteley, A.T. / Keszei, A.F.A. / Morehouse, B.R. / Mathews, I.T. / Antine, S.P. / Cabrera, V.J. / Kashin, D. / Niemann, P. / Jain, M. / Schwede, F. / Mekalanos, J.J. / Shao, S. ...Authors: Lowey, B. / Whiteley, A.T. / Keszei, A.F.A. / Morehouse, B.R. / Mathews, I.T. / Antine, S.P. / Cabrera, V.J. / Kashin, D. / Niemann, P. / Jain, M. / Schwede, F. / Mekalanos, J.J. / Shao, S. / Lee, A.S.Y. / Kranzusch, P.J.
History
DepositionMar 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 22, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: 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: SAVED domain-containing protein
B: SAVED domain-containing protein
C: SAVED domain-containing protein
D: SAVED domain-containing protein
E: SAVED domain-containing protein
F: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,83412
Polymers313,2586
Non-polymers5766
Water5,711317
1
A: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3062
Polymers52,2101
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3062
Polymers52,2101
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3062
Polymers52,2101
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3062
Polymers52,2101
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3062
Polymers52,2101
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3062
Polymers52,2101
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.718, 111.377, 173.298
Angle α, β, γ (deg.)90.000, 103.064, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
SAVED domain-containing protein


Mass: 52209.676 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: HMPREF0023_0548 / Production host: Escherichia coli (E. coli) / References: UniProt: C0VHC9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 0.2 M LiSO4, 16% PEG-3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→39.6 Å / Num. obs: 100775 / % possible obs: 88.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 45.38 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.9
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 5818 / CC1/2: 0.808

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VM6
Resolution: 2.6→39.6 Å / SU ML: 0.2736 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9673
RfactorNum. reflection% reflection
Rfree0.2286 1993 1.98 %
Rwork0.1942 --
obs0.1949 100725 88.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.5 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20800 0 30 317 21147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003721265
X-RAY DIFFRACTIONf_angle_d0.580528751
X-RAY DIFFRACTIONf_chiral_restr0.04273196
X-RAY DIFFRACTIONf_plane_restr0.00383681
X-RAY DIFFRACTIONf_dihedral_angle_d15.80727761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.2796880.23793954X-RAY DIFFRACTION50.04
2.67-2.740.2866880.23434628X-RAY DIFFRACTION58.71
2.74-2.820.30051150.2495407X-RAY DIFFRACTION68.12
2.82-2.910.27141240.25586093X-RAY DIFFRACTION77.3
2.91-3.010.24441340.24437202X-RAY DIFFRACTION90.13
3.01-3.130.28921600.23377892X-RAY DIFFRACTION99.84
3.13-3.280.30011630.23777900X-RAY DIFFRACTION99.68
3.28-3.450.27191520.22947928X-RAY DIFFRACTION99.77
3.45-3.660.25291630.20077914X-RAY DIFFRACTION99.65
3.66-3.950.22611540.18777846X-RAY DIFFRACTION98.7
3.95-4.340.22041680.16767975X-RAY DIFFRACTION99.98
4.34-4.970.18031640.1537954X-RAY DIFFRACTION99.78
4.97-6.260.2221570.18357967X-RAY DIFFRACTION99.17
6.26-39.60.16841630.16718072X-RAY DIFFRACTION99.44
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)
10.4341043218350.1377620389590.3758833202681.74743398402-0.2670305596240.8513297872320.07041735327430.196841686254-0.0272190506745-0.162778477625-0.0168792515258-0.254468069567-0.03275750471480.16415639856-0.05681979772890.2873392390820.006492508405030.06433687004190.420983027949-0.07043766539790.38922089129183.9376602033-17.465924906624.6087930846
21.480067293380.2881135718860.7782916994310.8834233196560.8611450136562.185169203220.1823780201580.0994672717252-0.158323187320.02546477154550.056160611537-0.2493720252560.2678673011740.302427304801-0.1860510837350.2717632353370.0203293016545-0.03037245701860.348225933216-0.02814522064730.494825964871100.318634375-25.147187802847.453499945
32.929072209360.05219267359960.6184569597192.144756065560.02619037934832.471530209490.19379756064-0.47361187916-0.2328392497910.3833251761590.0145206343051-0.1329917476630.431269043750.205272969006-0.2194013338160.443999255482-0.0297407865107-0.1445791940750.5255795865870.06587344204720.489722084943107.773302862-22.157959265769.378658031
40.702517841331-0.02175326125950.3903226383951.161741898990.1358521734931.106896583660.134750362616-0.0174499631049-0.1329903364090.0605629830275-0.05514906760240.08304785024530.159997649232-0.169880577151-0.06078601987040.255006426034-0.03524327807020.01260965460130.386566310160.01300066993250.33692143961135.4570679016-24.208737144547.2287235631
52.96899600782-0.134564508433-1.971100491342.396133186120.06135324587112.982951959790.1463212855940.1539688881030.147394164850.186394930984-0.1090533317510.754387694473-0.260148676333-0.767256675763-0.06906783238410.3688990009230.01480622620650.08134916330950.7026132224720.04973808897890.46686838689523.2674955895-4.1538947620953.0553584828
60.755521525679-0.2943238131150.415167559930.431317300469-0.6792728630572.030153569490.00149756744065-0.129692834007-0.04116637971250.1914283795480.004216003477660.112505354197-0.0969199513109-0.1983157812120.003987208916870.302750693961-0.07109044322580.04859364736690.3194647879190.01529146038890.31501684470540.3046953707-12.268834540472.3749185701
72.196542133330.001066334867260.9432378311930.503142724065-1.266677431613.97099018246-0.16287943387-0.8253309527250.4121713079870.6463276003510.09976994829130.326406038942-0.765954859688-1.46166581050.06068313218090.6696446860170.04952054667610.1212331804930.7030576087-0.1142811522140.43743087828333.5067400051-8.0232027928990.4260940199
82.80150511405-0.140156294405-0.6658749900671.74925494763-0.6622266141770.7712147146160.13773874356-0.7870065120060.2158473122540.8839094897140.0420673162969-0.693985409862-0.345988826911.06028921044-0.1810764248520.727519410729-0.215468457821-0.06828852231081.02700652521-0.09441341912160.50300119353753.5010855464-16.2872745501102.008356616
92.8281496263-0.2807899392390.08334325252982.63870755965-0.06828629584791.32818459384-0.0584732095271-0.4419797650230.07876184139230.508843552008-0.0764033104574-0.161733709404-0.4969751765670.3641177995570.1034428127760.807963624129-0.153377449807-0.003298859939610.824960924695-0.01963044552530.35833648687647.7208273543-11.059695606698.4166405053
102.39567847796-0.5125296620.2528693742780.8684634817760.5780632318882.472971942850.0579139531415-0.1567601259780.150746873460.190492355477-0.100222760603-0.211527779047-0.4069328201720.7207861465630.08389989470450.539082038357-0.2188714249480.02153598162940.6159878797150.04594662140280.32343126705850.7241324935-15.897123768490.2046101183
111.365816984580.2639947214870.1757144460190.4308550617550.2084372155531.35103807949-0.01504786068330.01651275725090.0598251325936-0.03126290726240.0428714341594-0.03302781769550.01602221444650.0202328715058-0.02031916359030.2835244252730.04164173147940.02873231652330.2218815199080.03672411982640.20320460899752.87534670573.160580475630.4913286267
122.07319745340.2227236856131.703525031551.191684610910.9242694808792.40077129107-0.1821956455270.117602346080.279435218967-0.1650773277920.1803866857950.0105113729996-0.4338012214780.0381972005096-0.04797432596770.404662060304-0.01470869031560.07513172956670.2472552710510.1105768031970.28242944655.999610006910.738476931426.1525244727
131.24207822454-0.644280068197-0.2039226460030.5840118148430.269308117021.338753668340.1006807964320.299947369660.078276031547-0.26061881992-0.02304274181530.006156439178130.00808734018652-0.0942029177773-0.08186917642780.39205196446-0.01855497676320.01124738636060.3055499411030.05046219679770.26679213713151.6094861782-7.7991238099.09670531135
142.431043916440.725289234889-0.7556776668141.45718558180.2450563311671.521496137040.1887578163871.28507967982-0.37882398376-0.682687099014-0.119305871203-0.2119966722970.4003483877130.369807354121-0.05889310282651.008175341440.223448972163-0.01102042510011.07437929963-0.175250407470.4676517275564.3844177244-19.0503874616-14.6492604689
152.82472918083-1.170470271860.6739734827110.776668807581-0.488503868991.525721738660.4516555372360.744206870221-0.330648476885-0.518821580446-0.238321330881-0.1223513246440.2558403138120.144760615576-0.168677816120.7636641769950.1461673131530.05811811858610.728844810072-0.1599320832440.42483663092967.3971518276-18.5558051543-5.05118200528
161.159834064480.084340383728-0.09415353727930.178283279307-0.2395486741291.38607531430.0269412463310.1493250717270.0614304261213-0.0525345828760.00147116949237-0.132568509061-0.06420194056170.0769050334341-0.02051095120390.249082828554-0.001426045107960.004369530881840.168092086678-0.03333886889840.30128816842276.4784555788-0.80087868534253.7255650331
170.837842523528-0.1434303505820.01039909184471.75567213240.6447407295211.884305651490.090815098197-0.1868837077310.07802514803760.468011405654-0.12702024148-0.151346948311-0.115492778021-0.04197645325830.03079516310860.450587136743-0.0128896100502-0.04230032975760.245815611756-0.008158967487760.35692760323566.86738500381.0283961007977.34312301
181.35165761329-0.8845851949840.3078213790531.501069294950.09795706892571.43357335310.0335207914305-0.04902506086250.07543649791030.0911702126411-0.003423991383040.049909657457-0.188844531965-0.0716916780436-0.01746932871220.269996725310.02433288645790.03453305251220.253446394699-0.009850869501320.28857096968350.442943798814.18571555357.4030597281
194.13761013113-1.63148488811.93724549472.92610285574-0.6640844596292.1461157063-0.0288626516848-0.4988299285150.309198468670.233974277786-0.0124253134960.209898878213-0.384527693626-0.6774581911840.05260589304440.6639700714490.2417534427070.1274961756440.638391091847-0.1081953900670.54749836341936.25280505828.904405684762.7411848842
202.484573171450.5328325772360.1376768590263.37344244829-0.03219509784342.23754124591-0.0469405190392-0.2919966760790.404730168323-0.1162686611740.2056996364890.169797601579-0.341009425025-0.322842723727-0.1854631983150.5282124160380.2328561883190.08095661124320.590048742965-0.05711090409480.63832491883332.067640609828.706961207261.6497325526
211.86585971484-0.6950658033310.9540869506691.526813475050.6343349071431.825148635080.0072203193783-0.151180105518-0.107318684345-0.179150011415-0.1326602235150.289781425466-0.223109754608-0.4297480157430.09556278551760.4303172179650.1632192451140.05751372726870.463971088301-0.03763310003420.50533569994836.112575724822.315368111855.1256962636
221.52164378513-0.2074602431720.1486690054790.436109077410.3176304159050.7694495765620.06495849148330.0308123595844-0.109623459187-0.0121382617507-0.0290012830354-0.06929797267250.126666376117-0.0789966489926-0.01652202204730.367618368143-0.00165878551505-0.02704567829250.2033491878520.02486906990650.30108679608363.3030057998-33.749989895762.7197905491
231.35378521971-0.1513934724310.2645976346660.525635610938-0.07806978040581.090461935180.104873369809-0.193693306779-0.1888089220940.252352227975-0.0657215738823-0.07939102399070.269972137899-0.159644946703-0.05013087819050.488406628408-0.0216733008756-0.03602773928340.2170599497080.04988436384590.37094996171566.7320104131-38.984071493967.9316248619
240.952684862626-0.1469671791610.6634051067211.242961707010.5700691002342.093688221590.1078403305980.041468083893-0.3603928926650.1764832734080.106359973402-0.2374059736880.4410407103490.233066160081-0.2025095806570.4002250433540.0704079146321-0.004903083255450.2686605343760.01640782636790.42923166953881.9509854617-47.89698705549.4083816554
250.9287697710290.4032286674570.3317775378121.816609314650.8094959871560.8589177870570.1288934427110.646282755075-0.9993445431890.02842504594320.420508023285-0.70114360410.6644339332880.64556442484-0.4973784453851.026184509970.307216853314-0.07250544601960.977576215471-0.4067363572231.2591908523893.0510064869-64.398974685434.8150670443
261.973868852850.2807587233751.48261006272.80142415832-0.01613209652732.79052038561-0.02198052736070.745091338314-0.664355702295-0.3341753053650.634334401532-0.7697386153810.3248807976970.92246985906-0.4292116891080.7856814957290.1655601987730.1031619046210.662699584133-0.3248044952820.89391083542786.6874272946-58.956050223832.1634442364
270.745891377108-0.202230548694-0.1305496378220.205494859032-0.2899545485261.703605196290.00348060542320.00390065914162-0.189445962197-0.002131581310920.06498406387710.03353475598670.253939348962-0.0851250922252-0.0593915926450.374329327834-0.0277866390755-0.04771322229480.29616555472-0.07038384905120.34889369967755.4071339794-42.416661931932.2181428047
280.8409749990010.1646910678830.4949017527330.5494701548450.6259653308592.05434771205-0.136737083720.16662586479-0.27271544910.1230980894390.114090450786-0.1029274477320.291740131194-0.0891157194190.02212888454250.485906046476-0.0242430192162-0.01710503433960.443934753696-0.1514196311440.43988840733558.9666856636-42.81097830858.483315066
292.28488851612-0.865648053281-0.5117035639980.813158310340.4299908664141.023942062950.0656637338330.414815881093-0.123596625039-0.158390614878-0.09325074501590.1572621972340.155879789851-0.3519433324340.03381943750770.385938805166-0.0344788583548-0.06705795074540.437754166925-0.06283937460670.32343860497435.9770688506-29.501479947914.4863987013
302.775432715950.0867183882718-0.362725374720.6242400778240.1092322792952.182924295090.3218470314331.210406944130.479754572054-0.464710156096-0.2021837615930.277461830812-0.499655034708-0.972581015523-0.1465745237110.5720796003960.173067615347-0.132050622541.301632324680.1484171849030.72438846012714.2850250286-18.0098381558.28736970081
313.538501950920.0481538280498-1.885310346233.645213229880.2791965377294.142999972070.7159728797180.4981600665490.992308997158-0.230241975411-0.621478475663-0.0948918411525-0.3553602014520.5087696774420.1037129253520.3850825943570.0934376101117-0.03578909094230.868312210090.2107429981970.69561573873119.328858063-17.924508581819.4121233455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 209 )
2X-RAY DIFFRACTION2chain 'A' and (resid 210 through 342 )
3X-RAY DIFFRACTION3chain 'A' and (resid 343 through 462 )
4X-RAY DIFFRACTION4chain 'B' and (resid 15 through 166 )
5X-RAY DIFFRACTION5chain 'B' and (resid 167 through 209 )
6X-RAY DIFFRACTION6chain 'B' and (resid 210 through 318 )
7X-RAY DIFFRACTION7chain 'B' and (resid 319 through 342 )
8X-RAY DIFFRACTION8chain 'B' and (resid 343 through 372 )
9X-RAY DIFFRACTION9chain 'B' and (resid 373 through 415 )
10X-RAY DIFFRACTION10chain 'B' and (resid 416 through 461 )
11X-RAY DIFFRACTION11chain 'C' and (resid 14 through 133 )
12X-RAY DIFFRACTION12chain 'C' and (resid 134 through 189 )
13X-RAY DIFFRACTION13chain 'C' and (resid 190 through 318 )
14X-RAY DIFFRACTION14chain 'C' and (resid 319 through 427 )
15X-RAY DIFFRACTION15chain 'C' and (resid 428 through 462 )
16X-RAY DIFFRACTION16chain 'D' and (resid 15 through 166 )
17X-RAY DIFFRACTION17chain 'D' and (resid 167 through 234 )
18X-RAY DIFFRACTION18chain 'D' and (resid 235 through 318 )
19X-RAY DIFFRACTION19chain 'D' and (resid 319 through 372 )
20X-RAY DIFFRACTION20chain 'D' and (resid 373 through 414 )
21X-RAY DIFFRACTION21chain 'D' and (resid 415 through 462 )
22X-RAY DIFFRACTION22chain 'E' and (resid 14 through 133 )
23X-RAY DIFFRACTION23chain 'E' and (resid 134 through 209 )
24X-RAY DIFFRACTION24chain 'E' and (resid 210 through 318 )
25X-RAY DIFFRACTION25chain 'E' and (resid 319 through 415 )
26X-RAY DIFFRACTION26chain 'E' and (resid 416 through 461 )
27X-RAY DIFFRACTION27chain 'F' and (resid 14 through 166 )
28X-RAY DIFFRACTION28chain 'F' and (resid 167 through 209 )
29X-RAY DIFFRACTION29chain 'F' and (resid 210 through 330 )
30X-RAY DIFFRACTION30chain 'F' and (resid 331 through 436 )
31X-RAY DIFFRACTION31chain 'F' and (resid 437 through 462 )

+
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