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- PDB-1qs1: CRYSTAL STRUCTURE OF VEGETATIVE INSECTICIDAL PROTEIN2 (VIP2) -

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Basic information

Entry
Database: PDB / ID: 1qs1
TitleCRYSTAL STRUCTURE OF VEGETATIVE INSECTICIDAL PROTEIN2 (VIP2)
ComponentsADP-RIBOSYLTRANSFERASE
KeywordsTOXIN / ALPHA-BETA PROTEIN / BINARY TOXIN / INSECTICIAL PROTEIN
Function / homology
Function and homology information


nucleotide binding / extracellular region
Similarity search - Function
Binary exotoxin A, clostridial type / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsHan, S. / Craig, J.A. / Putnam, C.D. / Carozzi, N.B. / Tainer, J.A.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Evolution and mechanism from structures of an ADP-ribosylating toxin and NAD complex.
Authors: Han, S. / Craig, J.A. / Putnam, C.D. / Carozzi, N.B. / Tainer, J.A.
History
DepositionJun 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ADP-RIBOSYLTRANSFERASE
B: ADP-RIBOSYLTRANSFERASE
C: ADP-RIBOSYLTRANSFERASE
D: ADP-RIBOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)210,0794
Polymers210,0794
Non-polymers00
Water27,0411501
1
A: ADP-RIBOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)52,5201
Polymers52,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-RIBOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)52,5201
Polymers52,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ADP-RIBOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)52,5201
Polymers52,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ADP-RIBOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)52,5201
Polymers52,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.900, 78.700, 105.900
Angle α, β, γ (deg.)108.65, 89.96, 90.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
ADP-RIBOSYLTRANSFERASE


Mass: 52519.730 Da / Num. of mol.: 4 / Fragment: MATURE VIP2 / Mutation: WILD TYPE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Bacillus cereus (bacteria)
References: UniProt: Q844J9*PLUS, NAD+ ADP-ribosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1501 / 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: 2.03 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG200, BOG, IMIDAZOLE, MALATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 mMTris1drop
330 %(w/v)PEG2001reservoir
41 %(w/v)octyl-beta-D-glucopyranoside1reservoir
5200 mMimidazole/malate1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 30, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 468627 / Num. obs: 215237 / % possible obs: 83.4 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 13
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.27 / % possible all: 69.2
Reflection
*PLUS
Num. measured all: 468627
Reflection shell
*PLUS
% possible obs: 69.2 % / Rmerge(I) obs: 0.27

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.5→20 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.269 21485 -RANDOM
Rwork0.235 ---
obs0.235 215166 81.4 %-
all-215166 --
Displacement parametersBiso mean: 24.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.143 Å20 Å20 Å2
2--1.527 Å20.225 Å2
3----1.384 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12824 0 0 1501 14325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.78
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.5→1.57 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.308 --
Rwork0.3 16476 -
obs--55.5 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.78
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Rfactor Rfree: 0.308 / Rfactor Rwork: 0.3

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