[English] 日本語
Yorodumi
- PDB-9g1y: Staphycoccus aureus MazF in complex with Nabobody 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g1y
TitleStaphycoccus aureus MazF in complex with Nabobody 3
Components
  • Endoribonuclease MazF
  • Nanobody 3
KeywordsTOXIN / Toxin-antitoxin system / Nanobody / Ribonuclease
Function / homology
Function and homology information


rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding
Similarity search - Function
mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor
Similarity search - Domain/homology
Endoribonuclease MazF
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69655353284 Å
AuthorsZorzini, V. / Haesaerts, S. / Loris, R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Vrije Universiteit BrusselSRP13 Belgium
CitationJournal: To Be Published
Title: Nanobody-mediated activation and inhibition of Staphylococcus aureus MazF
Authors: Prolic-Kalinsek, M. / Zorzini, V. / Haesaerts, S. / De Bruyn, P. / Loris, R.
History
DepositionJul 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoribonuclease MazF
B: Endoribonuclease MazF
C: Nanobody 3
D: Nanobody 3


Theoretical massNumber of molelcules
Total (without water)60,2874
Polymers60,2874
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-32 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.830, 59.540, 72.010
Angle α, β, γ (deg.)90.000, 103.390, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPILEILE(chain 'A' and (resid 0 through 2 or (resid 3...AA0 - 6113 - 74
121LYSLYSASNASN(chain 'A' and (resid 0 through 2 or (resid 3...AA63 - 11376 - 126
231ASPASPILEILE(chain 'B' and (resid 0 through 48 or (resid 49...BB0 - 6113 - 74
241LYSLYSASNASN(chain 'B' and (resid 0 through 48 or (resid 49...BB63 - 11376 - 126
152VALVALPROPRO(chain 'C' and (resid 4 through 20 or (resid 21...CC4 - 433 - 42
162GLUGLUSERSER(chain 'C' and (resid 4 through 20 or (resid 21...CC46 - 13245 - 131
272VALVALPROPRO(chain 'D' and ((resid 4 through 5 and (name N...DD4 - 433 - 42
282GLUGLUSERSER(chain 'D' and ((resid 4 through 5 and (name N...DD46 - 13245 - 131

NCS ensembles :
ID
1
2

-
Components

#1: Protein Endoribonuclease MazF / SaMazF / Toxin MazF / mRNA interferase MazF


Mass: 14952.206 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mazF, SA1873 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7A4G9, Hydrolases; Acting on ester bonds
#2: Antibody Nanobody 3


Mass: 15191.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M MgCl2, 0.1 M TRIS-HCl pH 8.5, 30% w/v PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.69655353284→45.3673456976 Å / Num. obs: 14597 / % possible obs: 97.5 % / Redundancy: 2.67 % / Biso Wilson estimate: 48.974417485 Å2 / CC1/2: 0.969 / Net I/σ(I): 4.49
Reflection shellResolution: 2.69655353284→2.86 Å / Redundancy: 2.67 % / Num. unique obs: 2309 / CC1/2: 0.408 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69655353284→45.3673456976 Å / SU ML: 0.457991705361 / Cross valid method: FREE R-VALUE / σ(F): 1.36881018944 / Phase error: 28.8649557855
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.274339099878 727 4.9873087741 %
Rwork0.215725686727 13850 -
obs0.218677503083 14577 97.563750753 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.774764644 Å2
Refinement stepCycle: LAST / Resolution: 2.69655353284→45.3673456976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3637 0 0 69 3706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008719424755463724
X-RAY DIFFRACTIONf_angle_d1.140205659015074
X-RAY DIFFRACTIONf_chiral_restr0.062635992007580
X-RAY DIFFRACTIONf_plane_restr0.00744860505213654
X-RAY DIFFRACTIONf_dihedral_angle_d13.93306752752216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6966-2.90470.3699664368411440.3054045099572739X-RAY DIFFRACTION97.332883187
2.9047-3.1970.3715831781081450.2787920205432751X-RAY DIFFRACTION98.3361629881
3.197-3.65940.3013476267831440.2433400995022782X-RAY DIFFRACTION97.7941176471
3.6594-4.60970.2445829092751470.1739351211712771X-RAY DIFFRACTION97.7554438861
4.6097-45.360.2278105434321470.1894836837152807X-RAY DIFFRACTION96.6306836768
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)
11.77631847889-1.268452082671.389536467553.155670378580.6718376360953.19357042912-0.0566595908103-0.2064647188980.07721291302850.06388797093460.04911724058790.243626469722-0.202750451163-0.4902939097890.01539721773220.2393663719860.01469862508770.05136902045740.3108480282640.001674669267080.35426936394913.843309845819.69286966778.9404814299
21.68106015424-0.979517117411-0.06211191025641.60273208428-0.7291801370272.73803577625-0.0928562222415-0.03616608047550.0337967563402-0.05066033697470.0612338089933-0.09605315534910.17769222438-0.003765824903190.03677588384640.272057198367-0.01143403637530.03252199056920.199012932932-0.04317901515640.28885164728528.01304896515.203437461337.57023968176
32.61538369561-0.5670021145811.659545147263.67043812391-0.710470363953.633850461920.1980853021450.9268906858860.0686922769449-0.939281467079-0.106769799610.3009211561860.2913229394340.803049869498-0.05540719125890.62026057269-0.00359601484787-0.1065910279960.8680816169620.03322170864960.5700212672869.286491581087.91756793316-21.7621724076
40.62664485622-0.2076476440351.004000453561.55516527925-1.029830881274.87898604937-0.0440186407047-0.08430419614120.2637475215870.0443699399056-0.0907239906326-0.01602808682-0.554306760179-0.07667350041430.09015946142330.4536286633360.003261888360280.03511682175310.334523488691-0.02110674418030.39189738664928.486411878612.406422887440.7105716806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

+
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