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- PDB-3o0p: Pilus-related Sortase C of Group B Streptococcus -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3o0p
TitlePilus-related Sortase C of Group B Streptococcus
ComponentsSortase family protein
KeywordsTRANSFERASE / HYDROLASE / sortase / pili assembly / pili subunits
Function / homology
Function and homology information


photosystem I reaction center / photosynthesis / chloroplast
Similarity search - Function
Sortase; Chain: A; / Sortase / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Electron transport accessory-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Photosystem I iron-sulfur center subunit VII
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMalito, E. / Spraggon, G.
CitationJournal: Faseb J. / Year: 2011
Title: Structure analysis and site-directed mutagenesis of defined key residues and motives for pilus-related sortase C1 in group B Streptococcus.
Authors: Cozzi, R. / Malito, E. / Nuccitelli, A. / D'Onofrio, M. / Martinelli, M. / Ferlenghi, I. / Grandi, G. / Telford, J.L. / Maione, D. / Rinaudo, C.D.
History
DepositionJul 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortase family protein


Theoretical massNumber of molelcules
Total (without water)24,0841
Polymers24,0841
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.087, 37.354, 51.242
Angle α, β, γ (deg.)90.00, 96.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sortase family protein


Mass: 24083.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: strain 515 (serotype Ia) / Gene: Pilus Island 2a (PI-2a), SAL_1484 / Plasmid: pET 54 DEST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q3DMP3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 1.78 Å3/Da / Density % sol: 30.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM Tris, 200mM NaOAc, 30% PEG-4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 40390 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 11.55 Å2 / Rsym value: 0.09 / Net I/σ(I): 38.2
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.412 / % possible all: 71.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W1J

2w1j


Resolution: 1.3→44.781 Å / SU ML: 0.09 / σ(F): 0.18 / Phase error: 16.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1817 1988 5.06 %
Rwork0.1548 --
obs0.1562 39285 92.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.71 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1155 Å20 Å21.2011 Å2
2--4.5578 Å2-0 Å2
3----3.4424 Å2
Refinement stepCycle: LAST / Resolution: 1.3→44.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 0 173 1640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011511
X-RAY DIFFRACTIONf_angle_d1.2792052
X-RAY DIFFRACTIONf_dihedral_angle_d14.971547
X-RAY DIFFRACTIONf_chiral_restr0.071240
X-RAY DIFFRACTIONf_plane_restr0.008264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2949-1.32720.2193830.16591574X-RAY DIFFRACTION55
1.3272-1.36310.17651000.14452170X-RAY DIFFRACTION75
1.3631-1.40320.19911080.1312455X-RAY DIFFRACTION86
1.4032-1.44850.17051290.12632617X-RAY DIFFRACTION91
1.4485-1.50030.15241480.12612762X-RAY DIFFRACTION96
1.5003-1.56040.17351450.12372773X-RAY DIFFRACTION97
1.5604-1.63140.17941320.12482821X-RAY DIFFRACTION98
1.6314-1.71740.16331890.12552813X-RAY DIFFRACTION99
1.7174-1.8250.17081670.1362823X-RAY DIFFRACTION99
1.825-1.96590.18451550.13892862X-RAY DIFFRACTION100
1.9659-2.16380.1691440.14342875X-RAY DIFFRACTION100
2.1638-2.47690.18691690.15622887X-RAY DIFFRACTION100
2.4769-3.12050.19141460.17022910X-RAY DIFFRACTION100
3.1205-44.80780.17891730.17572955X-RAY DIFFRACTION100

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