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- PDB-4g1h: Group B Streptococcus Pilus Island 1 Sortase C2 -

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Basic information

Entry
Database: PDB / ID: 4g1h
TitleGroup B Streptococcus Pilus Island 1 Sortase C2
ComponentsSortase family protein
KeywordsTRANSFERASE / CYSTEINE PROTEASE / EXTRACELLULAR
Function / homology
Function and homology information


hydrolase activity / membrane
Similarity search - Function
Sortase C / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Sortase family protein
Similarity search - Component
Biological speciesStreptococcus agalactiae serogroup V (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCozzi, R. / Prigozhin, D.M. / Alber, T.
CitationJournal: Plos One / Year: 2012
Title: Structural basis for group B streptococcus pilus 1 sortases C regulation and specificity.
Authors: Cozzi, R. / Prigozhin, D. / Rosini, R. / Abate, F. / Bottomley, M.J. / Grandi, G. / Telford, J.L. / Rinaudo, C.D. / Maione, D. / Alber, T.
History
DepositionJul 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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: Sortase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0572
Polymers24,0161
Non-polymers401
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.435, 60.435, 102.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Sortase family protein


Mass: 24016.465 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria)
Gene: SAG0648 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8E0S6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.94 Å3/Da / Density % sol: 36.71 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115889 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2010
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115889 Å / Relative weight: 1
ReflectionResolution: 1.8→30.22 Å / Num. obs: 17711 / Biso Wilson estimate: 27.14 Å2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30.22 Å / SU ML: 0.21 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 1716 9.98 %
Rwork0.212 --
obs0.216 17187 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.64 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 31.98 Å2
Baniso -1Baniso -2Baniso -3
1--5.1735 Å2-0 Å2-0 Å2
2---5.1735 Å20 Å2
3---10.347 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 1 91 1456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071393
X-RAY DIFFRACTIONf_angle_d1.0881894
X-RAY DIFFRACTIONf_dihedral_angle_d11.595521
X-RAY DIFFRACTIONf_chiral_restr0.07233
X-RAY DIFFRACTIONf_plane_restr0.004237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8650.32411330.29451197X-RAY DIFFRACTION75
1.865-1.93970.29451590.25411411X-RAY DIFFRACTION88
1.9397-2.02790.2911600.23451477X-RAY DIFFRACTION92
2.0279-2.13480.27291680.22921535X-RAY DIFFRACTION95
2.1348-2.26850.2931740.22411571X-RAY DIFFRACTION98
2.2685-2.44360.2641800.21911589X-RAY DIFFRACTION98
2.4436-2.68940.30731790.22911622X-RAY DIFFRACTION99
2.6894-3.07820.27611820.23731642X-RAY DIFFRACTION100
3.0782-3.8770.23721850.20151668X-RAY DIFFRACTION100
3.877-30.220.20031960.18271759X-RAY DIFFRACTION99

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