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- PDB-5cr6: Structure of pneumolysin at 1.98 A resolution -

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Basic information

Entry
Database: PDB / ID: 5cr6
TitleStructure of pneumolysin at 1.98 A resolution
ComponentsPneumolysin
KeywordsTOXIN / cholesterol-dependent cytolysin / virulence factor / Streptococcus pneumoniae
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
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 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.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust097828/z/11/z United Kingdom
Medical Research Council (United Kingdom)PhD project grant United Kingdom
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 1.1Aug 30, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / struct_sheet / struct_sheet_range
Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 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
D: Pneumolysin


Theoretical massNumber of molelcules
Total (without water)52,9251
Polymers52,9251
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.006, 127.710, 172.285
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pneumolysin / Thiol-activated cytolysin


Mass: 52925.086 Da / Num. of mol.: 1 / Mutation: N385D, C432A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ply, SPD_1726 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04IN8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris/Bicine pH 8.5 containing 30 mM CaCl2 30 mM MgCl2, 20% glycerol, 14% PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.94→43.1 Å / Num. obs: 42799 / % possible obs: 99.4 % / Redundancy: 6.2 % / Rsym value: 0.044 / Net I/σ(I): 39.7
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 5.84 / Rsym value: 0.461 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S3R

1s3r


Resolution: 1.98→43.071 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 2154 5.04 %
Rwork0.2485 40585 -
obs0.2494 42739 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.77 Å2 / Biso mean: 69.2103 Å2 / Biso min: 20.39 Å2
Refinement stepCycle: final / Resolution: 1.98→43.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3703 0 0 193 3896
Biso mean---52.05 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043786
X-RAY DIFFRACTIONf_angle_d0.8035146
X-RAY DIFFRACTIONf_chiral_restr0.03588
X-RAY DIFFRACTIONf_plane_restr0.003665
X-RAY DIFFRACTIONf_dihedral_angle_d13.7951393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.98-2.02610.30491250.29382673279899
2.0261-2.07680.29581310.29962724285599
2.0768-2.13290.34821290.30912503263296
2.1329-2.19570.33341680.292926332801100
2.1957-2.26650.3781650.31282692285799
2.2665-2.34750.31811440.295726352779100
2.3475-2.44150.34371320.295627372869100
2.4415-2.55260.33141570.293826362793100
2.5526-2.68720.32751420.279527462888100
2.6872-2.85550.3071390.285326752814100
2.8555-3.0760.32831380.27262679281798
3.076-3.38540.27211600.253727562916100
3.3854-3.8750.22451320.231727792911100
3.875-4.8810.20461490.206827672916100
4.881-43.08140.21961430.21622950309398
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)
10.1399-0.0257-0.19770.3583-0.29060.56340.21970.12740.0437-0.749-0.1144-0.0464-0.3199-0.1661-0.15923.0502-0.11080.33940.8192-0.01970.69768.669417.4068160.5499
21.7329-0.3576-1.06490.197-0.49924.911-0.1344-0.60560.3992-0.77250.3791-0.3648-0.68360.1712-0.31732.0326-0.08030.08351.1090.07230.96242.236435.9321193.0426
30.2330.1943-0.09761.1794-0.11550.07930.02210.1182-0.218-0.8328-0.10520.2986-0.4773-0.31380.00482.2847-0.0367-0.01630.3363-0.04040.63173.204110.3102171.4154
41.9056-0.1580.54660.30930.92493.5573-0.2086-0.71310.0528-0.99410.2374-0.1735-0.2744-0.43640.04511.10490.0277-0.00310.6988-0.10280.44662.671929.4374206.1751
52.5034-0.3561-0.65275.84742.2754.3889-0.1082-0.8536-0.45210.68040.1211-0.27460.8423-0.2521-0.03760.6057-0.0041-0.05760.63710.1460.44263.01495.5663205.6437
60.6263-0.35320.64973.72391.14441.7841-0.0067-0.2079-0.1275-1.12820.09670.0251-0.4958-0.3132-0.05210.6445-0.0647-0.04640.43950.01530.41622.03065.945187.7258
71.258-0.24230.82381.827-0.02854.4560.0751-0.0199-0.0589-0.35560.0068-0.0326-0.3839-0.9127-0.07520.15670.08650.02430.46430.02210.277910.608533.5932239.6816
81.9438-0.8971-0.97677.07163.81966.9472-0.0121-0.3155-0.3255-0.4633-0.0240.25920.0748-0.79570.00020.3269-0.0751-0.08070.48320.03040.37070.37057.1782195.0538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain D and (resid 1:21 or resid 207:226 or resid 336:343)D1 - 21
2X-RAY DIFFRACTION1chain D and (resid 1:21 or resid 207:226 or resid 336:343)D207 - 226
3X-RAY DIFFRACTION1chain D and (resid 1:21 or resid 207:226 or resid 336:343)D336 - 343
4X-RAY DIFFRACTION2chain D and (resid 22:33)D22 - 33
5X-RAY DIFFRACTION3chain D and (resid 57:101 or resid 112:119 or resid 201:206 or resid 227:241 or resid 329:335)D57 - 101
6X-RAY DIFFRACTION3chain D and (resid 57:101 or resid 112:119 or resid 201:206 or resid 227:241 or resid 329:335)D112 - 119
7X-RAY DIFFRACTION3chain D and (resid 57:101 or resid 112:119 or resid 201:206 or resid 227:241 or resid 329:335)D201 - 206
8X-RAY DIFFRACTION3chain D and (resid 57:101 or resid 112:119 or resid 201:206 or resid 227:241 or resid 329:335)D227 - 241
9X-RAY DIFFRACTION3chain D and (resid 57:101 or resid 112:119 or resid 201:206 or resid 227:241 or resid 329:335)D329 - 335
10X-RAY DIFFRACTION4chain D and (resid 34:56 or resid 344:360)D34 - 56
11X-RAY DIFFRACTION4chain D and (resid 34:56 or resid 344:360)D344 - 360
12X-RAY DIFFRACTION5chain D and (resid 253:284 or resid 306:328)D253 - 284
13X-RAY DIFFRACTION5chain D and (resid 253:284 or resid 306:328)D306 - 328
14X-RAY DIFFRACTION6chain D and (resid 102:111 or resid 120:145 or resid 155:189)D102 - 111
15X-RAY DIFFRACTION6chain D and (resid 102:111 or resid 120:145 or resid 155:189)D120 - 145
16X-RAY DIFFRACTION6chain D and (resid 102:111 or resid 120:145 or resid 155:189)D155 - 189
17X-RAY DIFFRACTION7chain D and (resid 361:471)D361 - 471
18X-RAY DIFFRACTION8chain D and (resid 146:154 or resid 190:200 or resid 242:252 or resid 285:305)D146 - 154
19X-RAY DIFFRACTION8chain D and (resid 146:154 or resid 190:200 or resid 242:252 or resid 285:305)D190 - 200
20X-RAY DIFFRACTION8chain D and (resid 146:154 or resid 190:200 or resid 242:252 or resid 285:305)D242 - 252
21X-RAY DIFFRACTION8chain D and (resid 146:154 or resid 190:200 or resid 242:252 or resid 285:305)D285 - 305

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