[English] 日本語
Yorodumi
- PDB-5k8j: Structure of Caulobacter crescentus VapBC1 (apo form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k8j
TitleStructure of Caulobacter crescentus VapBC1 (apo form)
Components
  • Ribonuclease VapC
  • VapB family protein
KeywordsHYDROLASE / PIN domain / toxin-antitoxin / ribonuclease / DNA-binding
Function / homology
Function and homology information


RNA nuclease activity / toxin activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
: / Antidote-toxin recognition MazE, bacterial antitoxin / 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
VapB family protein / Ribonuclease VapC
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsBendtsen, K.L. / Xu, K. / Luckmann, M. / Brodersen, D.E.
Funding support Denmark, 2items
OrganizationGrant numberCountry
The Lundbeck FoundationR173-2014-1182 Denmark
The Danish National Research FoundationDNRF120 Denmark
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding.
Authors: Bendtsen, K.L. / Xu, K. / Luckmann, M. / Winther, K.S. / Shah, S.A. / Pedersen, C.N.S. / Brodersen, D.E.
History
DepositionMay 30, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VapB family protein
B: Ribonuclease VapC
C: Ribonuclease VapC
D: VapB family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8596
Polymers47,6754
Non-polymers1842
Water6,341352
1
A: VapB family protein
B: Ribonuclease VapC
C: Ribonuclease VapC
D: VapB family protein
hetero molecules

A: VapB family protein
B: Ribonuclease VapC
C: Ribonuclease VapC
D: VapB family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,71812
Polymers95,3498
Non-polymers3684
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area29760 Å2
ΔGint-126 kcal/mol
Surface area30120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.290, 86.290, 113.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11D-13-

ASN

-
Components

#1: Protein VapB family protein


Mass: 9548.433 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: ATCC 19089 / CB15 / Gene: CC_0032 / Plasmid: pKW912HB / Production host: Escherichia coli B (bacteria) / Variant (production host): B834(DE3) / References: UniProt: Q9AC34
#2: Protein Ribonuclease VapC / RNase VapC / Toxin VapC


Mass: 14288.886 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: ATCC 19089 / CB15 / Gene: vapC, CC_0031 / Plasmid: pKW912HB / Production host: Escherichia coli B (bacteria) / Variant (production host): B834(DE3)
References: UniProt: Q9AC35, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 3 M NaCl, 0.1 M Bis-tris pH 5.5, 5 mM MgCl2, 5 mM beta-mercapto ethanol, 25% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.972 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.6→37.4 Å / Num. obs: 125126 / % possible obs: 100 % / Redundancy: 23.2 % / Biso Wilson estimate: 16.4 Å2 / CC1/2: 1 / Rsym value: 0.14 / Net I/σ(I): 22.8
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 22.8 % / Mean I/σ(I) obs: 1.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→37.4 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 16.65
RfactorNum. reflection% reflectionSelection details
Rfree0.1681 1975 3.09 %Random selection
Rwork0.1579 ---
obs0.1582 63905 98.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.21 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3113 0 12 352 3477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143254
X-RAY DIFFRACTIONf_angle_d1.1344415
X-RAY DIFFRACTIONf_dihedral_angle_d18.2431976
X-RAY DIFFRACTIONf_chiral_restr0.171509
X-RAY DIFFRACTIONf_plane_restr0.008576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.22981380.25324194X-RAY DIFFRACTION94
1.64-1.68440.23651290.23284205X-RAY DIFFRACTION95
1.6844-1.73390.2551360.21914263X-RAY DIFFRACTION95
1.7339-1.78990.21511370.20454304X-RAY DIFFRACTION96
1.7899-1.85390.21781390.1844330X-RAY DIFFRACTION97
1.8539-1.92810.21221380.16984406X-RAY DIFFRACTION98
1.9281-2.01580.16841440.15284437X-RAY DIFFRACTION99
2.0158-2.12210.15021440.1464440X-RAY DIFFRACTION99
2.1221-2.2550.14691390.14444485X-RAY DIFFRACTION100
2.255-2.42910.14841450.13694492X-RAY DIFFRACTION100
2.4291-2.67350.16171460.14894499X-RAY DIFFRACTION100
2.6735-3.06020.17021430.15454534X-RAY DIFFRACTION100
3.0602-3.85490.14321450.14164595X-RAY DIFFRACTION100
3.8549-37.37480.15911520.1514746X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.3497 Å / Origin y: 36.3746 Å / Origin z: 39.8612 Å
111213212223313233
T0.0801 Å2-0.0112 Å20.0043 Å2-0.1198 Å2-0.0057 Å2--0.1093 Å2
L1.1218 °2-0.2665 °20.0883 °2-0.534 °20.0233 °2--0.9846 °2
S0.0128 Å °0.0696 Å °-0.1145 Å °0.002 Å °-0.0306 Å °0.0101 Å °0.0731 Å °0.0497 Å °0.0117 Å °
Refinement TLS groupSelection details: all

+
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