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- PDB-4zgh: Structure of Sugar Binding Protein Pneumolysin -

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Basic information

Entry
Database: PDB / ID: 4zgh
TitleStructure of Sugar Binding Protein Pneumolysin
ComponentsPneumolysin
KeywordsSugar binding protein / toxin / beta-CFT
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
GOLD (I) CYANIDE ION / DI(HYDROXYETHYL)ETHER / Pneumolysin
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsParker, M.W. / Feil, S.C. / Morton, C.
CitationJournal: Sci Rep / Year: 2015
Title: Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation.
Authors: Lawrence, S.L. / Feil, S.C. / Morton, C.J. / Farrand, A.J. / Mulhern, T.D. / Gorman, M.A. / Wade, K.R. / Tweten, R.K. / Parker, M.W.
History
DepositionApr 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list ...diffrn_source / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / software / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Feb 13, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Sep 27, 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
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: Pneumolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,69210
Polymers53,6721
Non-polymers1,0219
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.857, 133.619, 220.442
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 / Thiol-activated cytolysin


Mass: 53671.816 Da / Num. of mol.: 1 / Fragment: UNP residues 2-470 / Mutation: N56S, K208R, E311D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: D39 / NCTC 7466 / Gene: ply, SPD_1726 / Plasmid: pQE-30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04IN8
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-AUC / GOLD (I) CYANIDE ION


Mass: 249.001 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2AuN2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.41 Å3/Da / Density % sol: 63.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8000, 10% glycerol, 10% ethylene glycol, 100 mM HEPES buffer, 5 mM potassium gold cyanide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.9→44.54 Å / Num. obs: 17539 / % possible obs: 99.4 % / Redundancy: 6 % / Biso Wilson estimate: 52.46 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.069 / Net I/σ(I): 12.2 / Num. measured all: 105956
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.9-3.076.10.6933.21659027150.8970.30296.6
8.69-44.545.10.04532.939247740.9990.02199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.9 Å41.87 Å
Translation2.9 Å41.87 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.4data scaling
PHASER2.5.1phasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HVN

1hvn


Resolution: 2.9→42.513 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 29.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3069 1577 5.04 %
Rwork0.1992 --
obs0.2045 17450 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→42.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 39 29 3812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0223849
X-RAY DIFFRACTIONf_angle_d1.9555212
X-RAY DIFFRACTIONf_dihedral_angle_d21.3611412
X-RAY DIFFRACTIONf_chiral_restr0.082591
X-RAY DIFFRACTIONf_plane_restr0.01671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.99410.39071310.2992600X-RAY DIFFRACTION95
2.9941-3.10110.37351500.26652832X-RAY DIFFRACTION100
3.1011-3.22520.29661400.23862595X-RAY DIFFRACTION100
3.2252-3.37190.29911430.22392683X-RAY DIFFRACTION100
3.3719-3.54960.31561180.21242865X-RAY DIFFRACTION100
3.5496-3.77190.30431610.1972571X-RAY DIFFRACTION100
3.7719-4.06290.31360.18552779X-RAY DIFFRACTION100
4.0629-4.47140.31641640.18142630X-RAY DIFFRACTION100
4.4714-5.11740.28841620.1592743X-RAY DIFFRACTION100
5.1174-6.44380.37341420.19962723X-RAY DIFFRACTION100
6.4438-42.51760.23841300.1842700X-RAY DIFFRACTION100
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)
1-0.0037-0.2912-0.09121.96731.6680.50430.12520.2812-0.2543-0.4853-0.1769-0.101-0.1443-0.24880.00010.63420.13930.01340.6788-0.09470.5498-10.219615.4922-51.7535
21.1203-0.7669-0.24783.17531.00781.64350.05770.212-0.3833-0.133-0.0174-0.13860.2728-0.2710.00560.309-0.0613-0.03160.4531-0.12090.4786-9.22857.2659-36.0319
30.160.1462-0.02480.1314-0.00630.0244-0.56740.1677-0.52450.2318-0.06730.34580.2247-0.2858-0.00121.25840.17270.00351.0788-0.21670.9204-10.1387-14.8034-62.2358
40.25330.1732-0.32560.4914-0.17930.3723-0.182-0.2497-0.4202-0.24030.4816-0.54571.27230.5675-0.00290.854-0.0165-0.06360.6661-0.16740.8304-2.6854-9.8837-44.0038
50.04-0.4396-0.41140.39610.68160.31190.34870.6584-0.0365-0.8232-0.2749-0.2536-0.0317-0.1578-0.04260.85460.10660.05560.1812-0.2210.5292-12.309610.0247-53.3389
61.14870.52840.1541.7216-0.35090.83470.1873-0.14480.32210.15370.06490.0923-0.56540.17630.00380.5584-0.06990.08930.38-0.07970.4426-1.0169-17.3354-97.391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -2:67 )A-2 - 67
2X-RAY DIFFRACTION2( CHAIN A AND RESID 68:252 )A68 - 252
3X-RAY DIFFRACTION3( CHAIN A AND RESID 253:281 )A253 - 281
4X-RAY DIFFRACTION4( CHAIN A AND RESID 282:329 )A282 - 329
5X-RAY DIFFRACTION5( CHAIN A AND RESID 330:361 )A330 - 361
6X-RAY DIFFRACTION6( CHAIN A AND RESID 362:470 )A362 - 470

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