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- PDB-5cr8: Structure of the membrane-binding domain of pneumolysin -

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Basic information

Entry
Database: PDB / ID: 5cr8
TitleStructure of the membrane-binding domain of pneumolysin
ComponentsPneumolysin
KeywordsTOXIN / cholesterol-dependent cytolysin / virulence factor / hydrolase
Function / homology
Function and homology information


hemolysis in another organism / cholesterol binding / : / toxin activity / killing of cells of another organism / membrane => GO:0016020 / 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
Thiol-activated cytolysin / Pneumolysin
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsMarshall, J.E. / Faraj, B.H.A. / Gingras, A.R. / Lonnen, R. / Sheikh, M.A. / El-Mezgueldi, M. / Moody, P.C.E. / Andrew, P.W. / Wallis, R.
CitationJournal: Sci Rep / Year: 2015
Title: The Crystal Structure of Pneumolysin at 2.0 angstrom Resolution Reveals the Molecular Packing of the Pre-pore Complex.
Authors: Marshall, J.E. / Faraj, B.H. / Gingras, A.R. / Lonnen, R. / Sheikh, M.A. / El-Mezgueldi, M. / Moody, P.C. / Andrew, P.W. / Wallis, R.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Pneumolysin
A: Pneumolysin


Theoretical massNumber of molelcules
Total (without water)26,4262
Polymers26,4262
Non-polymers00
Water2,972165
1
D: Pneumolysin


Theoretical massNumber of molelcules
Total (without water)13,2131
Polymers13,2131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Pneumolysin


Theoretical massNumber of molelcules
Total (without water)13,2131
Polymers13,2131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.680, 47.680, 97.539
Angle α, β, γ (deg.)90.000, 101.390, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-587-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 359 - 471 / Label seq-ID: 1 - 113

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAB
2chain DDA

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Components

#1: Protein Pneumolysin /


Mass: 13212.790 Da / Num. of mol.: 2 / Fragment: domain 4, UNP residues 359-471
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ply / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4GRG6, UniProt: Q04IN8*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 41.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG 2K MME containing 100 mM Potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.05→46.5 Å / Num. obs: 13832 / % possible obs: 99.4 % / Redundancy: 2.9 % / Rsym value: 0.091 / Net I/σ(I): 6.8
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 1349 / Rsym value: 0.451 / % possible all: 97.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CR6

5cr6


Resolution: 2.05→46.5 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2727 686 4.96 %
Rwork0.2239 13143 -
obs0.2263 13829 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.97 Å2 / Biso mean: 34.873 Å2 / Biso min: 8.47 Å2
Refinement stepCycle: final / Resolution: 2.05→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 0 165 2035
Biso mean---33.49 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051920
X-RAY DIFFRACTIONf_angle_d0.9462620
X-RAY DIFFRACTIONf_chiral_restr0.035284
X-RAY DIFFRACTIONf_plane_restr0.004330
X-RAY DIFFRACTIONf_dihedral_angle_d12.228692
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1050X-RAY DIFFRACTION5.921TORSIONAL
12D1050X-RAY DIFFRACTION5.921TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.20830.28131310.26032575270699
2.2083-2.43050.31411270.254726552782100
2.4305-2.78220.26731530.24032577273099
2.7822-3.50510.30491420.227126392781100
3.5051-46.540.2391330.19642697283099
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)
12.2787-0.5238-0.52.92190.42482.98160.25620.19520.13950.40560.1346-1.03490.5189-0.1524-0.06630.11560.00820.04260.1049-0.07470.1997-86.10633.6431221.8116
21.03440.0147-0.38751.0789-0.15146.39150.18660.58870.637-1.588-0.12030.15280.5156-0.66480.0293-0.49510.07120.20090.4840.19480.2371-91.527110.1565210.9186
30.91260.3822-0.06941.14630.18640.0509-0.04691.13270.3342-1.01730.2470.083-0.2359-0.02370.01140.7920.08730.0590.85560.17920.3348-94.131411.5182196.151
40.7481-0.75341.52981.0987-2.48394.7442-1.0053-0.6440.24980.5492-0.47720.58250.2843-1.4780.08120.1542-0.06860.24640.42960.2449-0.1311-95.53925.6653224.0914
51.71290.31850.22532.76720.322.59650.2120.22130.2112-0.1853-0.1373-0.1774-0.0449-0.21710.01840.1830.0309-0.00920.18810.00190.131-89.07478.3934217.0639
61.56340.6385-0.76752.9417-0.73444.5844-0.37470.3264-0.39760.92380.58040.4122-0.5957-1.1258-0.16990.21660.0081-0.01330.1282-0.06630.4498-91.27118.5195228.1306
71.6180.0232-0.76271.66770.38432.81010.3315-0.14560.32340.1120.6781-1.5807-0.11330.542-0.22670.2184-0.02060.01540.1287-0.1080.3632-79.83916.8915221.6275
81.4328-0.2353-0.05662.5382-0.91593.40240.0883-0.355-0.15350.0713-0.0222-0.1971-0.0702-0.1155-0.05840.074-0.0245-0.03380.18910.04980.1364-64.33811.9397216.3711
90.8162-0.19870.54520.046-0.12940.35590.10550.2762-0.1008-0.08490.0839-0.2027-0.01450.11-0.05490.6781-0.21910.05281.7812-0.61111.2787-69.4794.0156243.4582
101.405-0.090.06471.79460.39650.9256-0.0348-0.2825-0.03590.1437-0.0311-0.16470.1473-0.25220.11060.142-0.0247-0.01770.24910.04630.1411-67.504812.1504218.4388
111.25230.87160.83872.35161.66353.54390.1859-0.011-0.1678-0.2353-0.1328-0.06860.6971-0.2661-0.06850.2691-0.07650.07020.19950.00480.2544-66.70063.0395203.7783
121.1010.63770.53421.27870.632.4560.17280.0045-0.2452-0.08620.3287-0.51660.12540.6215-0.17250.15250.03450.02470.12480.02460.1551-57.261611.6293210.42
132.3810.89742.75733.09572.18588.0229-0.5456-0.02750.7050.0926-0.0763-1.6661-1.06950.70080.08290.2090.0781-0.04320.3142-0.06570.4063-52.538114.7117212.1178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 359 through 372 )D0
2X-RAY DIFFRACTION2chain 'D' and (resid 373 through 384 )D0
3X-RAY DIFFRACTION3chain 'D' and (resid 385 through 396 )D0
4X-RAY DIFFRACTION4chain 'D' and (resid 397 through 407 )D0
5X-RAY DIFFRACTION5chain 'D' and (resid 408 through 430 )D0
6X-RAY DIFFRACTION6chain 'D' and (resid 431 through 442 )D0
7X-RAY DIFFRACTION7chain 'D' and (resid 443 through 471 )D0
8X-RAY DIFFRACTION8chain 'A' and (resid 359 through 384 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 385 through 389 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 390 through 421 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 422 through 442 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 443 through 461 )A0
13X-RAY DIFFRACTION13chain 'A' and (resid 462 through 471 )A0

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