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- PDB-3ui3: Structural and Biochemical Characterization of HP0315 from Helico... -

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Basic information

Entry
Database: PDB / ID: 3ui3
TitleStructural and Biochemical Characterization of HP0315 from Helicobacter pylori as a VapD Protein with an Endoribonuclease Activity
ComponentsImmunoglobulin G-binding protein G, Virulence-associated protein D
KeywordsRNA BINDING PROTEIN / ferrodoxin-like fold / virulence associated protein D / ribonuclease
Function / homology
Function and homology information


nuclease activity / IgG binding / : / Hydrolases; Acting on ester bonds / RNA binding / extracellular region
Similarity search - Function
Endoribonuclease VapD / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / Alpha-Beta Plaits - #240 / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 ...Endoribonuclease VapD / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / Alpha-Beta Plaits - #240 / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease VapD / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus (bacteria)
Helicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsKwon, A.R. / Kim, J.H. / Lee, B.J.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural and biochemical characterization of HP0315 from Helicobacter pylori as a VapD protein with an endoribonuclease activity.
Authors: Kwon, A.R. / Kim, J.H. / Park, S.J. / Lee, K.Y. / Min, Y.H. / Im, H. / Lee, I. / Lee, K.Y. / Lee, B.J.
History
DepositionNov 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G, Virulence-associated protein D
B: Immunoglobulin G-binding protein G, Virulence-associated protein D


Theoretical massNumber of molelcules
Total (without water)37,4452
Polymers37,4452
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-15 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.810, 77.810, 106.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody Immunoglobulin G-binding protein G, Virulence-associated protein D / IgG-binding protein G


Mass: 18722.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The fusion protein of N-terminal tags (MSE)Q, the residues 304-357 from IgG-binding protein G, linker GS, residues 1-94 from vapD and C-terminal tags LEHHHHHH
Source: (gene. exp.) Streptococcus (bacteria), (gene. exp.) Helicobacter pylori (bacteria)
Strain: 26695 / Gene: HP_0315, spg, vapD / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19909, UniProt: O05728
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M (NH4)2SO4, 9% PEG3350, 5-8% glycerol, 100mM 2-(N-morpholino)ethanesulfonic acid', pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97951 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 9560 / Num. obs: 9541 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 57.51
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 11 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 5.25 / Num. unique all: 926 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→30 Å / Isotropic thermal model: anisotrophic / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2837 883 -random
Rwork0.2505 ---
obs0.2505 8605 90 %-
all-9560 --
Displacement parametersBiso mean: 95.9 Å2
Baniso -1Baniso -2Baniso -3
1-10.13 Å20 Å20 Å2
2--10.13 Å20 Å2
3----20.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 0 6 2048
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_deg0.62
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.032
RfactorNum. reflection
Rfree0.342 112
Rwork0.336 -
obs-1118

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