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- PDB-2gwm: Crystal structure of the Salmonella SpvB ATR Domain -

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Basic information

Entry
Database: PDB / ID: 2gwm
TitleCrystal structure of the Salmonella SpvB ATR Domain
Components65 kDa virulence protein
KeywordsTRANSFERASE / TOXIN / Salmonella / SpvB / ADP-ribosyltransferase
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase activity => GO:0106274 / NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / : / nucleotidyltransferase activity / toxin activity / nucleotide binding / extracellular region / cytoplasm
Similarity search - Function
Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / 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
Mono(ADP-ribosyl)transferase SpvB / Mono(ADP-ribosyl)transferase SpvB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsStebbins, C.E. / Margarit, S.M.
CitationJournal: Structure / Year: 2006
Title: A steric antagonism of actin polymerization by a salmonella virulence protein.
Authors: Margarit, S.M. / Davidson, W. / Frego, L. / Stebbins, C.E.
History
DepositionMay 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 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

Downloads & links

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Assembly

Deposited unit
A: 65 kDa virulence protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8503
Polymers22,6581
Non-polymers1922
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.585, 55.585, 143.577
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-99-

HOH

21A-298-

HOH

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Components

#1: Protein 65 kDa virulence protein


Mass: 22657.605 Da / Num. of mol.: 1 / Fragment: residues 391-590
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: mkaA / Production host: Escherichia coli (E. coli) / References: UniProt: P55220, UniProt: P21454*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.83 Å3/Da / Density % sol: 56.46 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorDate: Apr 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.48→40 Å / Num. obs: 41183 / % possible obs: 94.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.081 / Χ2: 1.302 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.48-1.532.20.33451360.93662
1.53-1.592.30.26170580.96183.7
1.59-1.672.70.2680300.95197.4
1.67-1.753.20.26283620.951100
1.75-1.863.70.25383500.966100
1.86-2.014.60.26283011.189100
2.01-2.215.80.22783431.03100
2.21-2.536.30.16483631.323100
2.53-3.196.20.08383181.663100
3.19-505.70.04583541.84899.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.848 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2063 5 %RANDOM
Rwork0.156 ---
all0.158 ---
obs0.157 41134 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.551 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.3 Å20 Å2
2--0.6 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 10 323 1925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221626
X-RAY DIFFRACTIONr_bond_other_d0.0030.021468
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9832197
X-RAY DIFFRACTIONr_angle_other_deg0.89833435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7124.86876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11915302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8931510
X-RAY DIFFRACTIONr_chiral_restr0.1410.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02308
X-RAY DIFFRACTIONr_nbd_refined0.2220.2354
X-RAY DIFFRACTIONr_nbd_other0.2040.21566
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2833
X-RAY DIFFRACTIONr_nbtor_other0.0890.2958
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4610.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1810.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.233
X-RAY DIFFRACTIONr_mcbond_it2.2361.51280
X-RAY DIFFRACTIONr_mcbond_other1.2081.5405
X-RAY DIFFRACTIONr_mcangle_it2.58321613
X-RAY DIFFRACTIONr_scbond_it4.5663722
X-RAY DIFFRACTIONr_scangle_it5.6564.5584
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 123 -
Rwork0.176 2274 -
obs-2397 78.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6379-0.51470.76370.8656-0.16433.55620.0546-0.21970.10510.0155-0.07520.0208-0.2072-0.22020.0206-0.0745-0.06240.00840.102-0.0144-0.02824.57124.61638.653
20.4556-0.14681.06780.2936-0.57993.83280.13180.01780.00940.0029-0.154-0.00260.07940.23570.0222-0.07610.02030.00610.0571-0.0073-0.037326.12822.10614.23
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11391 - 4581 - 68
22459 - 59069 - 200

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