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- PDB-1cdt: CARDIOTOXIN V4/II FROM NAJA MOSSAMBICA MOSSAMBICA: THE REFINED CR... -

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Basic information

Entry
Database: PDB / ID: 1cdt
TitleCARDIOTOXIN V4/II FROM NAJA MOSSAMBICA MOSSAMBICA: THE REFINED CRYSTAL STRUCTURE
ComponentsCARDIOTOXIN VII4
KeywordsCYTOTOXIN
Function / homology
Function and homology information


other organism cell membrane / toxin activity / killing of cells of another organism / extracellular region / membrane
Similarity search - Function
Snake cytotoxin, cobra-type / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Cytotoxin 4
Similarity search - Component
Biological speciesNaja mossambica (Mozambique cobra)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsRees, B. / Bilwes, A. / Samama, J.P. / Moras, D.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Cardiotoxin VII4 from Naja mossambica mossambica. The refined crystal structure.
Authors: Rees, B. / Bilwes, A. / Samama, J.P. / Moras, D.
History
DepositionMay 17, 1990Processing site: BNL
Revision 1.0Jul 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Category: pdbx_database_status / struct_conf / Item: _pdbx_database_status.process_site
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: CARDIOTOXIN VII4
B: CARDIOTOXIN VII4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6454
Polymers13,4552
Non-polymers1902
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.900, 73.900, 59.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Atom site foot note1: SOLVENT OCCUPANCIES WERE REFINED WITHOUT SETTING AN UPPER BOUND. VALUES LARGE THAN 1.0 ARE INDICATIVE OF THE INTRINSIC INACCURACY OF THIS PARAMETER AND OF ITS LARGE CORRELATION WITH THE TEMPERATURE FACTOR.

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Components

#1: Protein CARDIOTOXIN VII4


Mass: 6727.321 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naja mossambica (Mozambique cobra) / References: UniProt: P01452
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.39 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1MPD11
2potassium phosphate11

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.5→5 Å
Details: SOLVENT OCCUPANCIES WERE REFINED WITHOUT SETTING AN UPPER BOUND. VALUES LARGE THAN 1.0 ARE INDICATIVE OF THE INTRINSIC INACCURACY OF THIS PARAMETER AND OF ITS LARGE CORRELATION WITH THE TEMPERATURE FACTOR.
RfactorNum. reflection
obs0.197 4002
Refinement stepCycle: LAST / Resolution: 2.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 10 48 978
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_deg2.4
Refinement
*PLUS
σ(F): 3 / Highest resolution: 2.5 Å / Lowest resolution: 5 Å / Num. reflection obs: 4002 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d0.5

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