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- PDB-1ojz: The crystal structure of C3stau2 from S. aureus with NAD -

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Basic information

Entry
Database: PDB / ID: 1ojz
TitleThe crystal structure of C3stau2 from S. aureus with NAD
ComponentsADP-RIBOSYLTRANSFERASE
KeywordsTRANSFERASE / ADP-RIBOSYLTRANSFERASE
Function / homology
Function and homology information


NAD+-protein mono-ADP-ribosyltransferase activity / nucleotide binding / extracellular region
Similarity search - Function
Mono-ADP-ribosyltransferase C3/Edin / 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 / ADP-ribosyltransferase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.02 Å
AuthorsEvans, H.R. / Sutton, J.M. / Holloway, D.E. / Ayriss, J. / Shone, C.C. / Acharya, K.R.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The Crystal Structure of C3Stau2 from Staphylococcus Aureus and its Complex with Nad
Authors: Evans, H.R. / Sutton, J.M. / Holloway, D.E. / Ayriss, J. / Shone, C.C. / Acharya, K.R.
History
DepositionJul 16, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 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

Downloads & links

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Assembly

Deposited unit
A: ADP-RIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3302
Polymers23,6671
Non-polymers6631
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.900, 65.080, 75.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADP-RIBOSYLTRANSFERASE


Mass: 23666.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9ADS9
#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.: 135 / 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: 1.75 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.5 / Details: 30% PEG 8000 0.1M SODIUM CACODYLATE BUFFER PH 6.5
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.6 / PH range high: 6.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18.72-10.25 mg/mlprotein1drop
2100 mMsodium cacodylate1reservoirpH6.4-6.6
329-30 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97451
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 27, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97451 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 22478 / % possible obs: 96.9 % / Redundancy: 20 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 15.8
Reflection shellResolution: 2.02→2.09 Å / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.1 / % possible all: 96.6
Reflection
*PLUS
Highest resolution: 2.02 Å / Num. obs: 14088 / Num. measured all: 327780 / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.02→40 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 394174.98 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 925 -RANDOM
Rwork0.214 ---
obs0.214 12969 92.5 %-
Displacement parametersBiso mean: 24.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.02→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 44 135 1842
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_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
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: 2.02→2.15 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 138 6.8 %
Rwork0.241 1898 -
obs--88.9 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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