[English] 日本語
Yorodumi
- PDB-6nkl: 2.2 A resolution structure of VapBC-1 from nontypeable Haemophilu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nkl
Title2.2 A resolution structure of VapBC-1 from nontypeable Haemophilus influenzae
Components
  • Antitoxin VapB1
  • Ribonuclease VapC
KeywordsANTITOXIN / Toxin / H. influenzae / protein-protein complex
Function / homology
Function and homology information


RNA nuclease activity / toxin activity / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding
Similarity search - Function
SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / PIN domain / SpoVT-AbrB domain superfamily / VapC family / 5'-nuclease / PIN domain / PIN-like domain superfamily ...SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / PIN domain / SpoVT-AbrB domain superfamily / VapC family / 5'-nuclease / PIN domain / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonuclease VapC / Antitoxin / Ribonuclease VapC1 / Antitoxin VapB1
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Molinaro, A.L. / Daines, D.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)U01 DC014756 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: J.Bacteriol. / Year: 2019
Title: Crystal Structure of VapBC-1 from Nontypeable Haemophilus influenzae and the Effect of PIN Domain Mutations on Survival during Infection.
Authors: Molinaro, A.L. / Kashipathy, M.M. / Lovell, S. / Battaile, K.P. / Coussens, N.P. / Shen, M. / Daines, D.A.
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 6, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 11, 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: Ribonuclease VapC
B: Ribonuclease VapC
C: Antitoxin VapB1
D: Antitoxin VapB1


Theoretical massNumber of molelcules
Total (without water)55,5334
Polymers55,5334
Non-polymers00
Water1,04558
1
A: Ribonuclease VapC
B: Ribonuclease VapC
C: Antitoxin VapB1

D: Antitoxin VapB1


Theoretical massNumber of molelcules
Total (without water)55,5334
Polymers55,5334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area7650 Å2
ΔGint-61 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.880, 57.325, 175.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ribonuclease VapC / RNase VapC / Toxin VapC


Mass: 16894.568 Da / Num. of mol.: 2 / Fragment: VapB-1
Source method: isolated from a genetically manipulated source
Details: Residues at the C-terminus (LLEHHHHHH) are from the purification tag.
Source: (gene. exp.) Haemophilus influenzae (bacteria)
Gene: vapC1, vapC, BV136_01367, BVZ80_01200, CH628_04345, NCTC11872_02278
Plasmid: pDD686
Details (production host): The VapB-1 and VapC-1 complex was coexpressed
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2R3FUY7, UniProt: Q57122*PLUS, Hydrolases; Acting on ester bonds
#2: Protein Antitoxin VapB1


Mass: 10872.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues (MASMTGG QQMGRDPNSS S) at the N-terminus are from the cloning vector.
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: vapB1, BV136_01366, BVZ80_01199, CH628_04350 / Plasmid: pDD686
Details (production host): The VapB-1 and VapC-1 complex was coexpressed
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S9RDZ4, UniProt: Q57534*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% (w/v) PEG 4000, 0.1 M sodium acetate, 0.2 M ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.01 Å / Num. obs: 23388 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 37.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.168 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.2-2.2713.71.61319660.7841100
9.07-48.0110.70.0644070.996199.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.49 Å47.96 Å
Translation5.49 Å47.96 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.3data scaling
PHASER2.8.2phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ECD

5ecd


Resolution: 2.2→48.01 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 24.05
RfactorNum. reflection% reflection
Rfree0.2338 1166 5 %
Rwork0.186 --
obs0.1885 23312 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.71 Å2 / Biso mean: 43.4897 Å2 / Biso min: 20.7 Å2
Refinement stepCycle: final / Resolution: 2.2→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 0 58 3246
Biso mean---41.82 -
Num. residues----413
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.30020.28851480.225826922840
2.3002-2.42140.24981360.210727182854
2.4214-2.57310.2771470.209727312878
2.5731-2.77180.27841660.207427062872
2.7718-3.05070.27411160.201527652881
3.0507-3.4920.24761500.191627742924
3.492-4.39910.21421580.162128092967
4.3991-48.02290.19561450.175629513096

+
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://pdbjlvh1.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