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- PDB-1tet: CRYSTAL STRUCTURE OF AN ANTICHOLERA TOXIN PEPTIDE COMPLEX AT 2.3 ... -

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Basic information

Entry
Database: PDB / ID: 1tet
TitleCRYSTAL STRUCTURE OF AN ANTICHOLERA TOXIN PEPTIDE COMPLEX AT 2.3 ANGSTROMS
Components
  • CHOLERA TOXIN PEPTIDE 3 (CTP3)
  • IGG1 TE33 FAB (HEAVY CHAIN)
  • IGG1 TE33 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


toxin activity / killing of cells of another organism / extracellular region
Similarity search - Function
Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / Enterotoxin / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / : / : / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsShoham, M.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Crystal structure of an anticholera toxin peptide complex at 2.3 A.
Authors: Shoham, M.
#1: Journal: Proteins / Year: 1991
Title: Crystal Parameters and Molecular Replacement of an Anticholera Toxin Peptide Complex
Authors: Shoham, M. / Proctor, P. / Hughes, D. / Baldwin, E.T.
History
DepositionJun 21, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG1 TE33 FAB (LIGHT CHAIN)
H: IGG1 TE33 FAB (HEAVY CHAIN)
P: CHOLERA TOXIN PEPTIDE 3 (CTP3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4964
Polymers48,3043
Non-polymers1921
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-31 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.150, 110.610, 40.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO L 141 / 4: CIS PROLINE - PRO H 147 / 5: CIS PROLINE - PRO H 149
6: SER H 186 - PRO H 187 OMEGA = 145.25 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: CIS PROLINE - PRO H 189

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Components

#1: Antibody IGG1 TE33 FAB (LIGHT CHAIN)


Mass: 23872.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: PIR: PC4203
#2: Antibody IGG1 TE33 FAB (HEAVY CHAIN)


Mass: 22805.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 2072131
#3: Protein/peptide CHOLERA TOXIN PEPTIDE 3 (CTP3)


Mass: 1625.800 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P32890
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE NUMBERING OF TE33 RESIDUES IS ESSENTIALLY ACCORDING TO C.CHOTHIA AND A.M.LESK, J.MOL.BIOL. V. ...THE NUMBERING OF TE33 RESIDUES IS ESSENTIALLY ACCORDING TO C.CHOTHIA AND A.M.LESK, J.MOL.BIOL. V. 196, 901 (1987) WITH MODIFICATIONS INTRODUCED BY T.SCHERF, R.HILLER, F.NAIDER, M.LEVITT AND J.ANGLISTER, BIOCHEMISTRY V. 31, P. 6884 (1992).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal grow
*PLUS
pH: 4 / Method: unknown
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1PEG800011
2sodium citrate11

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 84 % / Rmerge(I) obs: 0.1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→5 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.148 -
obs0.148 13714
Refinement stepCycle: LAST / Resolution: 2.3→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 13 151 3541
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.58
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 5 Å / Num. reflection obs: 13714 / σ(F): 2 / Rfactor obs: 0.148
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.58

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