[English] 日本語
Yorodumi
- PDB-8smd: Structure of Clostridium botulinum prophage Tad1 in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8smd
TitleStructure of Clostridium botulinum prophage Tad1 in complex with 1''-3' gcADPR
ComponentsABC transporter ATPase
KeywordsUNKNOWN FUNCTION / gcADPR / Thoeris / anti-phage
Function / homologyChem-OJC / ABC transporter ATPase
Function and homology information
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLu, A. / Yirmiya, E. / Leavitt, A. / Avraham, C. / Osterman, I. / Garb, J. / Antine, S.P. / Mooney, S.E. / Hobbs, S.J. / Amitai, G. ...Lu, A. / Yirmiya, E. / Leavitt, A. / Avraham, C. / Osterman, I. / Garb, J. / Antine, S.P. / Mooney, S.E. / Hobbs, S.J. / Amitai, G. / Sorek, R. / Kranzusch, P.J.
Funding supportEuropean Union, Israel, Germany, United States, 5items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Israel Science Foundation Israel
German Research Foundation (DFG) Germany
The Pew Charitable Trusts United States
The G. Harold and Leila Y. Mathers Foundation United States
CitationJournal: Nature / Year: 2024
Title: Phages overcome bacterial immunity via diverse anti-defence proteins.
Authors: Yirmiya, E. / Leavitt, A. / Lu, A. / Ragucci, A.E. / Avraham, C. / Osterman, I. / Garb, J. / Antine, S.P. / Mooney, S.E. / Hobbs, S.J. / Kranzusch, P.J. / Amitai, G. / Sorek, R.
History
DepositionApr 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC transporter ATPase
B: ABC transporter ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7454
Polymers28,6622
Non-polymers1,0832
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-41 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.969, 95.969, 95.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-328-

HOH

-
Components

#1: Protein ABC transporter ATPase


Mass: 14331.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: FDB51_07880 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A846JTD7
#2: Chemical ChemComp-OJC / (2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione


Mass: 541.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21N5O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.65 % / Description: Cubes
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: magnesium chloride, Tris-HCl pH 8.5, 1,6-hexanediol

-
Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→42.92 Å / Num. obs: 17522 / % possible obs: 99.7 % / Redundancy: 13.5 % / Biso Wilson estimate: 53.87 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.025 / Net I/σ(I): 12.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 13.3 % / Num. unique obs: 1381 / CC1/2: 0.451 / Rpim(I) all: 0.698 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UAV

7uav


Resolution: 2.1→42.92 Å / SU ML: 0.3377 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.5479
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2361 877 5.02 %
Rwork0.2012 16604 -
obs0.203 17481 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 70 60 2114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00132088
X-RAY DIFFRACTIONf_angle_d0.39232812
X-RAY DIFFRACTIONf_chiral_restr0.0356303
X-RAY DIFFRACTIONf_plane_restr0.0026357
X-RAY DIFFRACTIONf_dihedral_angle_d12.5296792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.230.38161400.30212689X-RAY DIFFRACTION97.59
2.23-2.40.32261470.25282738X-RAY DIFFRACTION100
2.4-2.640.31671440.30272745X-RAY DIFFRACTION99.97
2.64-3.020.31811450.26682763X-RAY DIFFRACTION100
3.03-3.810.24381500.21512777X-RAY DIFFRACTION100
3.81-42.920.1851510.15462892X-RAY DIFFRACTION100
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)
10.1109616937810.0288701787673-0.05812053190620.08866618080560.1891186943640.246146380956-0.05325617689290.761464469743-0.526657399638-0.7767995143460.119872583368-0.352995722311-0.212008917069-0.2257599510195.45188767712E-50.654364679781-0.00353409185478-0.1144796289310.564198796946-0.07003833322380.6621042868339.08768524473-9.99876839869-41.1773824647
20.674529254622-0.84125041478-0.5546312196541.040027733360.5837607458661.35341453556-0.1947010837780.2712531987150.643786785633-0.00202278726494-0.0547973619730.226239292501-0.187024215205-0.231282136385-0.0007047501308280.5259025731290.00328997161197-0.0869311566360.4536843817530.01867953599410.5901486820246.415199950631.22308182384-36.6239748297
30.184507873144-0.0737263498024-0.249420991481-0.02734147499170.02176924335570.333398030451-0.478283142646-0.817997574830.4377954287060.2959608010930.436490571135-0.171555017166-0.1732248315390.32519297575-0.04585023230950.636037732188-0.00199625988502-0.2089622571720.505396552612-0.06994274006930.84731693440921.161681532110.7751113533-25.12090606
40.3082545661610.2852691994890.5916938523690.660847732714-0.84874554220.0639401068988-0.0693348256725-0.3909057024470.1182293676480.267768352672-0.0188357826112-0.1923211634490.1093845297080.0967189048686-0.05320181076460.5235677167950.0504462483397-0.07290811424030.47820643498-0.06638965054710.5430390901220.8637529553-9.1407681299-22.0273983733
50.377940912842-0.6870693246930.6695090349140.951232779675-0.7955890488090.778671793194-0.482696276985-0.22164812750.2437576402630.2206416183410.3393905522470.197308645874-0.139905783183-0.1325440001469.88038961562E-50.6330915879340.0520707106188-0.04313953923720.58051718526-0.1323648535720.55948409708911.0385579037-4.09751771485-15.3088683611
66.94561496776-1.56798718316-1.057643874234.514877178332.097019143590.967124812628-0.208247855853-1.43332350806-0.3072865409391.302427388520.3660447603830.561031874494-0.539779735493-0.0390802274972-0.03923157484881.052735816390.0204424267368-0.008310565956580.785268716771-0.1705794928590.76796052504312.585325962613.1965770267-13.8751325903
70.406802657650.495768981235-0.566041710711.68828684333-0.7917590345641.4035637397-0.3216656128540.04792063823981.00895845849-0.3373411854170.003800437362540.831879638956-0.137576088372-0.5997069537020.0539268163890.4653239675010.10149254216-0.03911449766740.522065894647-0.06283746536310.7154552734632.32272419962-3.78266499074-23.6472767622
80.0338656603673-0.06402964475520.004799133465270.0981703146611-0.02522027923350.05194194212190.403897782934-1.31670023050.1449816519610.331060222246-0.1071480579030.8312788857010.3451540888050.156204551289-0.0009626367213890.72149949639-0.1478387317770.07865412875620.59626862229-0.0441642629310.754722926827-7.88482156414-16.0249597898-30.0438077696
9-0.06026231571430.021848480559-0.2441749181020.156132508398-0.2178161476690.28853503289-0.3614443738020.3104616884250.212721076016-0.1194188670220.2485470643950.06280934815130.1484020417080.0860674947304-8.02701019388E-50.486603809594-0.00711775374811-0.05347761573760.420063764049-0.02363988263850.54579114571116.4846056422-4.55446626165-32.5482888205
100.7275777919950.1094099465220.05277669438450.418662091376-0.09514934181230.6296320570580.08884411840820.0455268356575-0.199601024053-0.19487002178-0.110018873187-0.06709382968620.301785616520.1699708023451.14814793532E-50.4969451702950.0476079037656-0.03308610619660.37679284636-0.008816034766680.43259320722813.0061835736-18.7280002237-31.7308523517
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 14 )AA2 - 141 - 13
22chain 'A' and (resid 15 through 52 )AA15 - 5214 - 51
33chain 'A' and (resid 53 through 68 )AA53 - 6852 - 67
44chain 'A' and (resid 69 through 125 )AA69 - 12568 - 124
55chain 'B' and (resid 3 through 36 )BC3 - 361 - 34
66chain 'B' and (resid 37 through 47 )BC37 - 4735 - 45
77chain 'B' and (resid 48 through 57 )BC48 - 5746 - 55
88chain 'B' and (resid 58 through 62 )BC58 - 6256 - 60
99chain 'B' and (resid 63 through 90 )BC63 - 9061 - 88
1010chain 'B' and (resid 91 through 125 )BC91 - 12589 - 123

+
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