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- PDB-4g1j: Sortase C1 of GBS Pilus Island 1 -

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Basic information

Entry
Database: PDB / ID: 4g1j
TitleSortase C1 of GBS Pilus Island 1
ComponentsSortase family protein
KeywordsTRANSFERASE / CYSTEINE PROTEASE / EXTRACELLULAR
Function / homology
Function and homology information


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: 1.75 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 / 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

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Assembly

Deposited unit
A: Sortase family protein
B: Sortase family protein


Theoretical massNumber of molelcules
Total (without water)49,6362
Polymers49,6362
Non-polymers00
Water6,305350
1
A: Sortase family protein


Theoretical massNumber of molelcules
Total (without water)24,8181
Polymers24,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sortase family protein


Theoretical massNumber of molelcules
Total (without water)24,8181
Polymers24,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.977, 48.467, 59.369
Angle α, β, γ (deg.)87.31, 76.85, 72.64
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Sortase family protein


Mass: 24818.207 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 42-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria)
Gene: SAG0647 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8E0S7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.1 Å3/Da / Density % sol: 41.41 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.75→46.25 Å / Num. obs: 31194 / Biso Wilson estimate: 20.56 Å2

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(PHENIX.REFINE: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.25 Å / SU ML: 0.2 / σ(F): 0.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 1486 4.76 %
Rwork0.172 --
obs0.173 31194 77 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.31 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 28.58 Å2
Baniso -1Baniso -2Baniso -3
1--7.6185 Å2-2.815 Å20.2164 Å2
2--0.1292 Å27.1253 Å2
3---7.4892 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 0 350 3502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073220
X-RAY DIFFRACTIONf_angle_d1.0254366
X-RAY DIFFRACTIONf_dihedral_angle_d12.8051204
X-RAY DIFFRACTIONf_chiral_restr0.071501
X-RAY DIFFRACTIONf_plane_restr0.004565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.81590.2897490.2162805X-RAY DIFFRACTION21
1.8159-1.88860.207700.19061320X-RAY DIFFRACTION35
1.8886-1.97450.2441940.1932075X-RAY DIFFRACTION53
1.9745-2.07860.23881630.17623246X-RAY DIFFRACTION84
2.0786-2.20890.20081820.17113611X-RAY DIFFRACTION93
2.2089-2.37940.22181820.17353644X-RAY DIFFRACTION94
2.3794-2.61890.24531870.1833697X-RAY DIFFRACTION96
2.6189-2.99770.20431870.18633759X-RAY DIFFRACTION97
2.9977-3.77660.18341860.16713744X-RAY DIFFRACTION98
3.7766-46.250.18051860.15853807X-RAY DIFFRACTION98

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