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- PDB-5k8j: Structure of Caulobacter crescentus VapBC1 (apo form) -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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