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- PDB-4y4q: Crystal structure of sortase B from Type II pilus of Streptococcu... -

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Basic information

Entry
Database: PDB / ID: 4y4q
TitleCrystal structure of sortase B from Type II pilus of Streptococcus pneumoniae
ComponentsSortase, SrtB family
KeywordsHYDROLASE / pilus / virulence factor / sortase / Type II pilus
Function / homology
Function and homology information


Sortase B family / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Sortase, SrtB family / :
Similarity search - Component
Biological speciesStreptococcus pneumoniae PCS8235 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.162 Å
AuthorsShaik, M.M. / Dessen, A. / Di Guilmi, A.M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11- BSV8-005-02 France
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A Structural Snapshot of Type II Pilus Formation in Streptococcus pneumoniae.
Authors: Shaik, M.M. / Lombardi, C. / Maragno Trindade, D. / Fenel, D. / Schoehn, G. / Di Guilmi, A.M. / Dessen, A.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 23, 2015Group: Database references
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model / Author supporting evidence
Category: atom_site / pdbx_audit_support / pdbx_validate_close_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.1Jan 10, 2024Group: 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
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: Sortase, SrtB family
B: Sortase, SrtB family


Theoretical massNumber of molelcules
Total (without water)55,0292
Polymers55,0292
Non-polymers00
Water2,774154
1
A: Sortase, SrtB family


Theoretical massNumber of molelcules
Total (without water)27,5151
Polymers27,5151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sortase, SrtB family


Theoretical massNumber of molelcules
Total (without water)27,5151
Polymers27,5151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.150, 101.140, 143.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sortase, SrtB family


Mass: 27514.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae PCS8235 (bacteria)
Gene: PCS8235_00725 / Plasmid: pET151 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M7N1R6, UniProt: A0A0M3KL14*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 54.22 % / Description: Stack of Plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.4 M Sodium Formate, 0.1 M Citric Acid / Temp details: Temperature control crystal growth room

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0045 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0045 Å / Relative weight: 1
ReflectionResolution: 2.16→41.31 Å / Num. obs: 27931 / % possible obs: 95.7 % / Redundancy: 3.5 % / Rsym value: 0.078 / Net I/σ(I): 9.33
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.43 / % possible all: 83.41

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QPS

3qps


Resolution: 2.162→41.315 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 1410 5.05 %Random selection
Rwork0.1882 ---
obs0.1904 27894 95.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.162→41.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 0 154 2959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082869
X-RAY DIFFRACTIONf_angle_d1.1273886
X-RAY DIFFRACTIONf_dihedral_angle_d14.0651026
X-RAY DIFFRACTIONf_chiral_restr0.078417
X-RAY DIFFRACTIONf_plane_restr0.004514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.162-2.23930.35771240.28642288X-RAY DIFFRACTION83
2.2393-2.32890.28881240.24522389X-RAY DIFFRACTION88
2.3289-2.43490.27631290.22582478X-RAY DIFFRACTION91
2.4349-2.56330.28321520.21222624X-RAY DIFFRACTION96
2.5633-2.72390.25931400.21072729X-RAY DIFFRACTION99
2.7239-2.93410.27981420.20462722X-RAY DIFFRACTION100
2.9341-3.22930.23781370.19032787X-RAY DIFFRACTION100
3.2293-3.69630.18351460.16662790X-RAY DIFFRACTION100
3.6963-4.65590.17481670.14182776X-RAY DIFFRACTION100
4.6559-41.32240.24981490.19172901X-RAY DIFFRACTION99
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)
11.4193-1.6881-0.12243.9290.77146.0986-0.1423-0.50870.27270.927-0.01730.5054-0.0652-0.4330.04210.4517-0.08820.09910.3907-0.07570.351121.074437.258827.8045
24.54352.59630.35755.4968-0.3434.07920.03110.0811-0.01930.18910.0498-0.10760.0507-0.0382-0.07790.2134-0.03590.03040.2024-0.01520.213326.539531.650313.5809
32.69120.2427-0.26948.9667-0.23265.5297-0.23760.39360.7783-0.28130.10590.8014-0.2227-0.43120.12130.2764-0.0632-0.00930.20780.03430.260222.263334.491212.5037
40.9853-1.41610.32223.6051-1.44716.0755-0.1096-0.3123-0.33991.07940.0558-0.62650.11890.49230.0580.4856-0.0683-0.02170.40220.03280.262116.1180.741527.4834
53.35651.77260.18495.07980.41594.0340.1152-0.17620.03690.268-0.02420.13220.079-0.0005-0.08370.2156-0.04860.040.2016-0.01350.175510.64356.126113.5415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 92 )
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 191 )
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 216 )
4X-RAY DIFFRACTION4chain 'B' and (resid 32 through 91 )
5X-RAY DIFFRACTION5chain 'B' and (resid 92 through 216 )

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