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- PDB-1qmd: calcium bound closed form alpha-toxin from Clostridium perfringens -

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Basic information

Entry
Database: PDB / ID: 1qmd
Titlecalcium bound closed form alpha-toxin from Clostridium perfringens
ComponentsPHOSPHOLIPASE C
KeywordsHYDROLASE / ZINC PHOSPHOLIPASE C / GANGRENE DETERMINANT / C2 DOMAIN / CA AND MEMBRANE BINDING.
Function / homology
Function and homology information


calcium-dependent phospholipase C activity / phospholipase C / phosphatidylcholine phospholipase C activity / hemolysis in another organism / toxin activity / hydrolase activity / 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
Phospholipase C / Phospholipase C
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNaylor, C.E. / Miller, J. / Titball, R.W. / Basak, A.K.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Characterisation of the Calcium-Binding C-Terminal Domain of Clostridium Perfringens Alpha-Toxin
Authors: Naylor, C.E. / Jepson, M. / Crane, D.T. / Titball, R.W. / Miller, J. / Basak, A.K. / Bolgiano, B.
#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.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallisation and Preliminary X-Ray Diffraction Studies of Alpha-Toxin from Two Different Strains (Nctc-8237 and Cer89L43) of Clostridium Perfringens
Authors: Basak, A.K. / Howells, A. / Eaton, J.T. / Moss, D.S. / Naylor, C. / Miller, J. / Titball, R.W.
History
DepositionSep 27, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOLIPASE C
B: PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,65812
Polymers85,1562
Non-polymers50210
Water5,639313
1
A: PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8296
Polymers42,5781
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8296
Polymers42,5781
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)149.890, 149.890, 192.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99858, -0.05276, -0.00747), (-0.05275, -0.99861, 0.00159), (-0.00754, -0.0012, -0.99997)
Vector: 5.33481, 172.99655, 160.89508)

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Components

#1: Protein PHOSPHOLIPASE C / PLC / PHOSPHATIDYLCHOLINE / ALPHA-TOXIN / HEMOLYSIN / CHOLINEPHOSPHOHYDROLASE / LECITHINASE


Mass: 42577.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: NCTC8237 / Plasmid: PUC18 / Cellular location (production host): PERIPLASMIC / Gene (production host): CPA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109
References: UniProt: P15310, UniProt: Q0TV31*PLUS, phospholipase C
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Sequence details27 RESIDUES AT START OF SEQUENCE ARE A SIGNAL PEPTIDE NOT PRESENT IN MATURE, ACTIVE FOLDED PROTEIN.

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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: 2.45 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.7
Details: PROTEIN WAS CRYSTALLISED BY HANGING DROP FROM 1.8-2.0 M NACL IN 0.1 M NA ACETATE, PH 4.7 OR 4.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.8 M1reservoirNaCl
2100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 / Details: MIRRORS
RadiationMonochromator: GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 42803 / % possible obs: 97.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 6.5 / % possible all: 92.4
Reflection
*PLUS
Num. measured all: 134096
Reflection shell
*PLUS
% possible obs: 92.4 % / Num. unique obs: 5854 / Num. measured obs: 16154

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNS0.9phasing
X-PLORphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CALCIUM-FREE, CLOSED ALPHA-TOXIN PDB CODE: 1QM6

1qm6


Resolution: 2.2→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 6850999.89 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: XPLOR AND REFMAC ALSO USED IN EARLIER STAGES OF REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2115 5.1 %RANDOM
Rwork0.198 ---
obs0.198 41734 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.2 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.66 Å2-1.87 Å20 Å2
2---4.66 Å20 Å2
3---9.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6012 0 10 313 6335
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.442
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.792.5
Refine LS restraints NCSRms dev position: 0.13 Å / Weight position: 200
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 368 5.4 %
Rwork0.214 6471 -
obs--98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLPARAM19.SOL
X-RAY DIFFRACTION3PARAM19.IONPARAM19.ION
X-RAY DIFFRACTION4PARAM_ALPHA_SUBMISSION.CDTOP_ALPHA_SUBMISSION.CD
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.183 / Rfactor Rfree: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13

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