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- PDB-1m3i: Perfringolysin O, new crystal form -

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Basic information

Entry
Database: PDB / ID: 1m3i
TitlePerfringolysin O, new crystal form
Componentsperfringolysin O
KeywordsTOXIN / pore forming toxin
Function / homology
Function and homology information


hemolysis in another organism / cholesterol binding / membrane => GO:0016020 / toxin activity / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain ...Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / 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 / Glutaredoxin / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Perfringolysin O / Perfringolysin O
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRossjohn, J. / Parker, M. / Polekhina, G. / Feil, S. / Tweten, R.
CitationJournal: To be Published
Title: Structural Snapshots in the Molecular Mechanism of PFO Revealed
Authors: Rossjohn, J. / Parker, M. / Polekhina, G. / Feil, S. / Tweten, R.
History
DepositionJun 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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
Remark 999SEQUENCE ACCORDING TO THE AUTHOR, THIS REPRESENTS AN ERROR IN THE INITIAL PROTEIN SEQUENCE ...SEQUENCE ACCORDING TO THE AUTHOR, THIS REPRESENTS AN ERROR IN THE INITIAL PROTEIN SEQUENCE DETERMINATION. REFER TO PDB ENTRY 1PFO.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: perfringolysin O
B: perfringolysin O
C: perfringolysin O
D: perfringolysin O


Theoretical massNumber of molelcules
Total (without water)210,2864
Polymers210,2864
Non-polymers00
Water5,260292
1
A: perfringolysin O


Theoretical massNumber of molelcules
Total (without water)52,5721
Polymers52,5721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: perfringolysin O


Theoretical massNumber of molelcules
Total (without water)52,5721
Polymers52,5721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: perfringolysin O


Theoretical massNumber of molelcules
Total (without water)52,5721
Polymers52,5721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: perfringolysin O


Theoretical massNumber of molelcules
Total (without water)52,5721
Polymers52,5721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.410, 130.410, 129.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
perfringolysin O


Mass: 52571.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: pfoa / Production host: Escherichia coli (E. coli) / References: UniProt: P19995, UniProt: P0C2E9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 8% peg 8000, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 59700 / Num. obs: 59700 / % possible obs: 97.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.8
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.571 / % possible all: 97.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1pfo

1pfo


Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1632 -random
Rwork0.233 ---
all-53577 --
obs-51945 95.2 %-
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14628 0 0 292 14920

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