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- PDB-6nkl: 2.2 A resolution structure of VapBC-1 from nontypeable Haemophilu... -

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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 ...: / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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 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

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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

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Phasing

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

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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

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