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- PDB-1olp: Alpha Toxin from Clostridium Absonum -

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Basic information

Entry
Database: PDB / ID: 1olp
TitleAlpha Toxin from Clostridium Absonum
ComponentsALPHA-TOXIN
KeywordsHYDROLASE / ZINC PHOSPHOLIPASE C / GAS GANGRENE DETERMINANT / MEMBRANE BINDING / CALCIUM BINDING
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 SARDINIENSE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBriggs, D.C. / Basak, A.K.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Clostridium Absonum Alpha-Toxin: New Insights Into Clostridial Phospholipase C Substrate Binding and Specificity
Authors: Clark, G. / Briggs, D.C. / Karasawa, T. / Wang, X. / Cole, A. / Maegawa, T. / Jayasekera, P. / Naylor, C. / Miller, J. / Moss, D. / Nakamura, S. / Basak, A.K. / Titball, R.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Structure of the Key Toxin in Gas Gangrene
Authors: Naylor, C.E. / Eaton, J.T. / Howells, A. / Justin, N. / Moss, D.S. / Titball, R.W. / Basak, A.K.
History
DepositionAug 11, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2003Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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
C: ALPHA-TOXIN
D: ALPHA-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,12124
Polymers171,0154
Non-polymers1,10620
Water6,521362
1
A: ALPHA-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0306
Polymers42,7541
Non-polymers2765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0306
Polymers42,7541
Non-polymers2765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ALPHA-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0306
Polymers42,7541
Non-polymers2765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ALPHA-TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0306
Polymers42,7541
Non-polymers2765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.956, 193.592, 92.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.07531, -0.99655, -0.03482), (-0.99716, -0.07523, -0.00361), (0.00098, 0.03499, -0.99939)56.97738, 59.28033, 137.35834
2given(-0.10368, 0.80299, 0.5869), (-0.76618, -0.44074, 0.46767), (0.6342, -0.40119, 0.66094)-4.36955, 21.49468, -29.45985
3given(0.13296, 0.88791, 0.44038), (-0.53496, 0.43833, -0.72228), (-0.83435, -0.13955, 0.53328)4.5218, 93.1437, 71.55604

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Components

#1: Protein
ALPHA-TOXIN


Mass: 42753.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM SARDINIENSE (bacteria) / Description: CLOSTRIDIUM ABSONUM / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8GCY3, phospholipase C
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.42 Å3/Da / Density % sol: 48.79 %
Crystal growpH: 5.5
Details: 100MM NA-CITRATE 5.6, 30% PEG 4000,200MM AMMONIUM ACETATE, pH 5.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
3100 mMsodium citrate1reservoirpH5.6
430 %(w/v)PEG40001reservoir
5200 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 15, 2000 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→29.784 Å / Num. obs: 53292 / % possible obs: 96.1 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 8
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 2 / % possible all: 90
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 56134 / Num. measured all: 623268 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
AMoREmodel building
REFMAC5.1.24refinement
SCALAdata scaling
MOLREPphasing
CNSphasing
COMOphasing
AMoREphasing
EPMRphasing
XFITphasing
Ophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CA1 WITH LOOPS OMITTED

1ca1


Resolution: 2.5→29.75 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.818 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.786 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED RESIDUES/ATOMS WERE OMITTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2840 5.1 %RANDOM
Rwork0.178 ---
obs0.181 53292 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11910 0 20 362 12292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02112253
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210003
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9116669
X-RAY DIFFRACTIONr_angle_other_deg0.819323389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15651472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.21708
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213965
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022564
X-RAY DIFFRACTIONr_nbd_refined0.1970.22650
X-RAY DIFFRACTIONr_nbd_other0.2250.211246
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.26732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2411
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.226
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5771.57319
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.087211723
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.27334934
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1074.54946
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 186
Rwork0.217 3527
Refinement
*PLUS
Rfactor Rfree: 0.233 / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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