1CA1

ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS

> Summary

Summary for 1CA1

DescriptorALPHA-TOXIN
Functional Keywordszinc phospholipase c, gangrene determinant, c2 domain, ca and membrane binding, hydrolase
Biological sourceClostridium perfringens
Total number of polymer chains1
Total molecular weight44030.61
Authors
Naylor, C.E.,Basak, A.K.,Titball, R.W. (deposition date: 1998-04-22, release date: 1999-05-04, modification date: 2011-11-16)
Primary citation
Naylor, C.E.,Eaton, J.T.,Howells, A.,Justin, N.,Moss, D.S.,Titball, R.W.,Basak, A.K.
Structure of the key toxin in gas gangrene.
Nat.Struct.Biol., 5:738-746, 1998
PubMed: 9699639
DOI: 10.1038/1447
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.9 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.243122.7%3.8%10.3%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1ca1
no rotation
Molmil generated image of 1ca1
rotated about x axis by 90°
Molmil generated image of 1ca1
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AALPHA-TOXINpolymer37042616.31
UniProt (P15310)
Pfam (PF00882)
Pfam (PF01477)
UniProt (by SIFTS) (P0C216)
Clostridium perfringensPHOSPHOLIPASE C
ZINC IONnon-polymer65.41
CADMIUM IONnon-polymer112.412
waterwater18.0173

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight42616.3
Non-Polymers*Number of molecules13
Total molecular weight1414.3
All*Total molecular weight44030.6
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.9 Å)
Cell axes61.300177.30079.100
Cell angles90.0090.0090.00
SpacegroupC 2 2 21
Resolution limits25.00 - 1.90
the highest resolution shell value1.970 - 1.900
R-factor0.208
R-work0.20800
the highest resolution shell value0.323
R-free0.25400
the highest resolution shell value0.333
RMSD bond length0.012
RMSD bond angle2.117 (23.262*)

Data Collection Statistics

Resolution limits40.00 - 1.90
the highest resolution shell value -
Number of reflections30175
Number of measurements202958*
Rmerge_l_obs0.065
the highest resolution shell value0.157
Completeness87.5 (91.0*)
Redundancy5.26
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1Vapor diffusion, hanging drop*7.520**

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11drop0.05 (M)
21dropNa-HEPES0.1 (M)
31reservoirsodium acetate1 (M)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005576cellular_componentextracellular region
A0034480molecular_functionphosphatidylcholine phospholipase C activity
A0008270molecular_functionzinc ion binding
A0044179biological_processhemolysis in other organism
A0009405biological_processpathogenesis
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
ZN13ZINC BINDING SITE AT ACTIVE SITE.
ChainResidue
ATRP1
AHIS11
AASP130

CD232ND ZINC BINDING SITE, CONTAINING CD FROM CRYSTALLISATION BUFFER.
ChainResidue
AHIS136
AHIS148
AGLU152

CD343ND ZINC BINDING SITE, CONTAINING CD FROM CRYSTALLISATION BUFFER.
ChainResidue
AASP130
AHIS68
AHIS126
AASP56

CD43CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
ChainResidue
AGLY168
ACYS169
AHIS207

CD53CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
ChainResidue
ACYS169
AGLU173
AASP216

CD63CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
ChainResidue
AGLU173
AHIS212
AASP216

CD72CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
ChainResidue
AASP174
AASP178

CD82CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
ChainResidue
AHIS241
AGLU245

CD92CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
ChainResidue
AASP293
AASP63

C102CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
ChainResidue
AHIS46
AGLU359

C111CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
ChainResidue
AGLU157

C122CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE. POSSIBLE CA BINDING SITE.
ChainResidue
AASP273
AASN297

CA14POSSIBLE CA BINDING SITE. CURRENTLY LOW OCCUPANCY CD ION (RESIDUE 383)
ChainResidue
AASP336
AALA337
AASP269
AGLY271

AC15BINDING SITE FOR RESIDUE ZN A 371
ChainResidue
ATRP1
AHIS11
AASP130
ACD
AHOH

AC25BINDING SITE FOR RESIDUE CD A 372
ChainResidue
AHIS136
AHIS148
AGLU152
AHOH
AHOH

AC36BINDING SITE FOR RESIDUE CD A 373
ChainResidue
AASP56
AHIS68
AHIS126
AASP130
AZN
AHOH

AC46BINDING SITE FOR RESIDUE CD A 374
ChainResidue
AGLY168
ACYS169
AHIS207
AHOH
AHOH
AHOH

AC55BINDING SITE FOR RESIDUE CD A 375
ChainResidue
ACYS169
AGLU173
AASP216
AHOH
AHOH

AC65BINDING SITE FOR RESIDUE CD A 376
ChainResidue
AGLU173
AHIS212
AASP216
AHOH
AHOH

AC76BINDING SITE FOR RESIDUE CD A 377
ChainResidue
AASP174
AASP178
AHOH
AHOH
AHOH
AHOH

AC83BINDING SITE FOR RESIDUE CD A 378
ChainResidue
AHIS241
AGLU245
AHOH

AC93BINDING SITE FOR RESIDUE CD A 379
ChainResidue
AASP63
AASP293
AHOH

BC14BINDING SITE FOR RESIDUE CD A 380
ChainResidue
AHIS46
AGLU359
AHOH
AHOH

BC26BINDING SITE FOR RESIDUE CD A 381
ChainResidue
AGLU157
AGLU157
AHOH
AHOH
AHOH
AHOH

BC38BINDING SITE FOR RESIDUE CD A 382
ChainResidue
AASP273
AASP273
AASN297
AASN297
AHOH
AHOH
AHOH
AHOH

BC46BINDING SITE FOR RESIDUE CD A 383
ChainResidue
AASP269
AGLY271
AASP336
AALA337
AHOH
AHOH

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS003841Prokaryotic zinc-dependent phospholipase C signature. H-Y-x-[GT]-D-[LIVMAF]-[DNSH]-x-P-x-H-[PA]-x-N
ChainResidueDetails
ANA*

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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails
CSA11Annotated By Reference To The Literature 1ah7
ChainResidueDetails
AASP56

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Catalytic Information from CATRES

site_idNumber of ResiduesDetails
extCATRES11Mapped from 1ah7 to 1ca1 using BLAST. All catalytic residues present. Original details record follows: a catalytic site defined by CATRES, Medline 89159438, 94047060
ChainResidueDetails
AASP55activates water, cofactor or residue. deprotonates water molecule for nucleophilic attack on phosphate

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb1ca1.ent.gz (73.36 KB)
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all (no-compress)pdb1ca1.ent (327.8 KB)
header onlypdb1ca1.ent.gz (9.4 KB)
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PDBx/mmCIF1ca1.cif.gz (89.86 KB)
PDBMLall1ca1.xml.gz (136.58 KB)
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no-atom1ca1-noatom.xml.gz (26.41 KB)
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ext-atom1ca1-extatom.xml.gz (74.56 KB)
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PDBMLplusall1ca1-plus.xml.gz (138.78 KB)
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no-atom1ca1-plus-noatom.xml.gz (28.6 KB)
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add only1ca1-add.xml.gz (2.19 KB)
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RDF1ca1.rdf.gz (53.28 KB)
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Structure factorsr1ca1sf.ent.gz (411.47 KB)
Biological unit (PDB format)1ca1.pdb1.gz (66.39 KB) (A)
*author defined assembly, 1 molecule(s) (monomeric)
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1ca1.pdb2.gz (129.81 KB) (A)
*software defined assembly, 2 molecule(s) (dimeric)
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1ca1.pdb3.gz (130.03 KB) (A)
*software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF1ca1​_validation.pdf.gz (256.63 KB)
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PDF-full1ca1​_full​_validation.pdf.gz (266.63 KB)
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XML1ca1​_validation.xml.gz (19.31 KB)
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PNG1ca1​_multipercentile​_validation.png.gz (158.26 KB)
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SVG1ca1​_multipercentile​_validation.svg.gz (949 B)
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Sequence (fasta)1ca1​_seq.txt
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