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- PDB-1qs2: CRYSTAL STRUCTURE OF VIP2 WITH NAD -

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Basic information

Entry
Database: PDB / ID: 1qs2
TitleCRYSTAL STRUCTURE OF VIP2 WITH NAD
ComponentsADP-RIBOSYLTRANSFERASE
KeywordsTOXIN / ALPHA-BETA PROTEIN / PROTEIN-NAD COMPLEX / BINARY TOXIN
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Vip2Ac
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-RIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2202
Polymers45,5561
Non-polymers6631
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.673, 70.564, 142.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein ADP-RIBOSYLTRANSFERASE


Mass: 45556.496 Da / Num. of mol.: 1 / Fragment: MATURE VIP2 / Mutation: WILD TYPE
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH NAD / Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Bacillus cereus (bacteria)
References: UniProt: Q844J9*PLUS, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG200, 2-METHYL 2,4-PENTANEDIOL, NAD, BIS-TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 118889 / Num. obs: 15370 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.309 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 118889
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 99.9 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.7→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1508 -RANDOM
Rwork0.207 ---
obs0.207 15323 99.2 %-
all-15323 --
Displacement parametersBiso mean: 40.05 Å2
Baniso -1Baniso -2Baniso -3
1-2.666 Å20 Å20 Å2
2---2.177 Å20 Å2
3----0.489 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3200 0 44 145 3389
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.45
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.14
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: 2.7→2.82 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.384 --
Rwork0.324 1626 -
obs--96.4 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.26
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Rfactor Rfree: 0.384 / Rfactor Rwork: 0.324

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