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- PDB-4qqq: Crystal structure of pneumolysin from Streptococcus pneumoniae, i... -

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Basic information

Entry
Database: PDB / ID: 4qqq
TitleCrystal structure of pneumolysin from Streptococcus pneumoniae, in complex with mannose as a component of cell membrane
ComponentsPneumolysin
KeywordsTOXIN / PLY / Cholesterol-dependent Cytolysin / Cholesterol/mannose binding
Function / homology
Function and homology information


cholesterol binding / toxin activity / killing of cells of another organism / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Perfringolysin, domain 4 / Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / Immunoglobulin-like ...Perfringolysin, domain 4 / Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Thiol-activated cytolysin
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPark, S.A. / Lee, K.S.
CitationJournal: To be Published
Title: Crystal structure of pneumolysin from Streptococcus pneumoniae, in complex with mannose as a component of cell membrane
Authors: Park, S.A. / Lee, K.S.
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Pneumolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7123
Polymers54,3521
Non-polymers3602
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.679, 157.454, 211.325
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pneumolysin


Mass: 54351.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ply / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2XU26
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.78 Å3/Da / Density % sol: 67.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Bicine-Tris, 30% EDO_P8K, 0.12M monosaccharides, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.2398 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 26806 / % possible obs: 88.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 34.93 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.079 / Net I/σ(I): 11.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2154 / Rsym value: 0.318 / % possible all: 74.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4QQA

4qqa


Resolution: 2.5→40.82 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 1335 5 %RANDOM
Rwork0.2125 ---
all0.2154 ---
obs0.2154 26691 88.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 24 121 3967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093924
X-RAY DIFFRACTIONf_angle_d1.3285334
X-RAY DIFFRACTIONf_dihedral_angle_d18.2451432
X-RAY DIFFRACTIONf_chiral_restr0.093612
X-RAY DIFFRACTIONf_plane_restr0.005685
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5001-2.58940.35161030.27752037203775
2.5894-2.69310.30971200.26512178217877
2.6931-2.81560.36761110.24972149214977
2.8156-2.9640.2791190.23872295229583
2.964-3.14970.26681350.2292510251088
3.1497-3.39270.26881400.23182637263194
3.3927-3.73390.27991430.20052730273096
3.7339-4.27380.25331480.18532839283998
4.2738-5.38250.21121510.17842869286998
5.3825-40.82540.29051650.21593112311299

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