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- PDB-1ojq: The crystal structure of C3stau2 from S. aureus -

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Basic information

Entry
Database: PDB / ID: 1ojq
TitleThe crystal structure of C3stau2 from S. aureus
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
ADP-ribosyltransferase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 15, 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 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4May 8, 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

Downloads & links

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Assembly

Deposited unit
A: ADP-RIBOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)23,6671
Polymers23,6671
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.616, 64.525, 74.984
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 22, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 22478 / % possible obs: 98.9 % / Redundancy: 20 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 20
Reflection shellResolution: 1.68→1.74 Å / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 5.3 / % possible all: 97.5
Reflection
*PLUS
Highest resolution: 1.68 Å / Num. obs: 22619 / % possible obs: 99.4 % / Num. measured all: 409845 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 97.5 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 5.3

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→50 Å / Num. parameters: 7863 / Num. restraintsaints: 6859 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: CNS (BRUNGER ET AL) WAS USED IN THE INITIAL STAGES OF REFINEMENT. RESIDUES 197-199 ARE SLIGHTLY DISORDERED AND MODELLED ON THE BASIS OF WEAK DENSITY. THE EXTREMITIES OF SIDE CHAINS 85, ...Details: CNS (BRUNGER ET AL) WAS USED IN THE INITIAL STAGES OF REFINEMENT. RESIDUES 197-199 ARE SLIGHTLY DISORDERED AND MODELLED ON THE BASIS OF WEAK DENSITY. THE EXTREMITIES OF SIDE CHAINS 85, 94,170 AND 200 HAVE BEEN MODELLED AT ZERO OCCUPENCY DUE TO INSUFFICIENT DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 872 -RANDOM
obs0.17 -99.5 %-
all-22327 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 5 / Occupancy sum non hydrogen: 1934.98
Refinement stepCycle: LAST / Resolution: 1.68→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 0 284 1934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0271
X-RAY DIFFRACTIONs_zero_chiral_vol0.037
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.062
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.3

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