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- PDB-1kho: Crystal Structure Analysis of Clostridium perfringens alpha-Toxin... -

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Basic information

Entry
Database: PDB / ID: 1kho
TitleCrystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP
Componentsalpha-toxin
KeywordsTOXIN / N-terminal alpha-helix / C-terminal beta-sheet
Function / homology
Function and homology information


phospholipase C / phosphatidylcholine phospholipase C activity / toxin activity / killing of cells of another organism / extracellular region / zinc ion binding
Similarity search - Function
Zinc-dependent phospholipase C / Phospholipase C/D / Zinc dependent phospholipase C / Prokaryotic zinc-dependent phospholipase C signature. / Prokaryotic zinc-dependent phospholipase C domain profile. / Zinc dependent phospholipase C (alpha toxin) / P1 Nuclease / P1 Nuclease / Phospholipase C/P1 nuclease domain superfamily / PLAT/LH2 domain ...Zinc-dependent phospholipase C / Phospholipase C/D / Zinc dependent phospholipase C / Prokaryotic zinc-dependent phospholipase C signature. / Prokaryotic zinc-dependent phospholipase C domain profile. / Zinc dependent phospholipase C (alpha toxin) / P1 Nuclease / P1 Nuclease / Phospholipase C/P1 nuclease domain superfamily / PLAT/LH2 domain / Lipoxygenase-1 / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJustin, N. / Moss, D.S. / Titball, R.W. / Basak, A.K.
CitationJournal: Biochemistry / Year: 2002
Title: The first strain of Clostridium perfringens isolated from an avian source has an alpha-toxin with divergent structural and kinetic properties.
Authors: Justin, N. / Walker, N. / Bullifent, H.L. / Songer, G. / Bueschel, D.M. / Jost, H. / Naylor, C. / Miller, J. / Moss, D.S. / Titball, R.W. / Basak, A.K.
History
DepositionNov 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha-toxin
B: alpha-toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2358
Polymers84,8432
Non-polymers3926
Water2,738152
1
A: alpha-toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6184
Polymers42,4211
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha-toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6184
Polymers42,4211
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.230, 117.230, 220.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein alpha-toxin


Mass: 42421.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CPA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9RF12
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 4.47 Å3/Da / Density % sol: 72.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: Na acetate, acetone, Na cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.5 Msodium acetate1reservoir
26-10 %2-propanol1reservoiror acetate
30.1 Msodium cacodylate1reservoirpH6.5
410 mg/mlprotein1drop
510 mMTris-HCl1droppH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 60799 / Num. obs: 59406 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.6
Reflection shellResolution: 2.4→2.65 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 6.8 / % possible all: 91.3
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 97.8 % / Num. measured all: 1381901 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Lowest resolution: 2.53 Å / % possible obs: 91.3 % / Rmerge(I) obs: 0.187

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 4828 -Random
Rwork0.2098 ---
all-60799 --
obs-59406 97.7 %-
Refine analyzeLuzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5990 0 6 152 6148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.49
X-RAY DIFFRACTIONc_bond_d0.01
Refinement
*PLUS
% reflection Rfree: 8 % / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.88

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