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- PDB-1b44: CRYSTAL STRUCTURE OF THE B SUBUNIT OF HEAT-LABILE ENTEROTOXIN FRO... -

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Basic information

Entry
Database: PDB / ID: 1b44
TitleCRYSTAL STRUCTURE OF THE B SUBUNIT OF HEAT-LABILE ENTEROTOXIN FROM E. COLI CARRYING A PEPTIDE WITH ANTI-HSV ACTIVITY
ComponentsPROTEIN (B-POL SUBUNIT OF HEAT-LABILE ENTEROTOXIN)
KeywordsTOXIN / B SUBUNIT / HEAT-LABILE ENTEROTOXIN ANTI-HSV
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Heat-labile enterotoxin B chain / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.3 Å
AuthorsMatkovic-Calogovic, D. / Loregian, A. / D'Acunto, M.R. / Battistutta, R. / Tossi, A. / Palu, G. / Zanotti, G.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Crystal structure of the B subunit of Escherichia coli heat-labile enterotoxin carrying peptides with anti-herpes simplex virus type 1 activity.
Authors: Matkovic-Calogovic, D. / Loregian, A. / D'Acunto, M.R. / Battistutta, R. / Tossi, A. / Palu, G. / Zanotti, G.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Specific Inhibition of Herpes Virus Replication by Receptor-Mediated Entry of an Antiviral Peptide Linked to Escherichia Coli Enterotoxin B Subunit
Authors: Marcello, A. / Loreggian, A. / Cross, A. / Marsden, H. / Hirst, T.R. / Palu, G.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Structure of Escherichia Coli Heat-Labile Enterotoxin, a Close Relative of Cholera Toxin
Authors: Sixma, T.K. / Kalk, K.H. / Van Zanten, B.A.M. / Dauter, Z. / Kingma, J. / Witholt, B. / Hol, W.G.J.
History
DepositionJan 4, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: PROTEIN (B-POL SUBUNIT OF HEAT-LABILE ENTEROTOXIN)
E: PROTEIN (B-POL SUBUNIT OF HEAT-LABILE ENTEROTOXIN)
F: PROTEIN (B-POL SUBUNIT OF HEAT-LABILE ENTEROTOXIN)
G: PROTEIN (B-POL SUBUNIT OF HEAT-LABILE ENTEROTOXIN)
H: PROTEIN (B-POL SUBUNIT OF HEAT-LABILE ENTEROTOXIN)


Theoretical massNumber of molelcules
Total (without water)71,4675
Polymers71,4675
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-60 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.100, 127.100, 176.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.423739, 0.714311, -0.55696), (-0.304147, 0.691398, 0.655334), (0.853194, -0.108293, 0.510228)15.5337, 46.9454, -76.6349
2given(-0.51287, 0.857222, -0.046195), (0.226285, 0.186901, 0.955962), (0.828106, 0.479831, -0.289833)98.1824, 24.0957, -107.3382
3given(-0.515539, 0.222609, 0.827445), (0.855658, 0.185007, 0.483344), (-0.045487, 0.957193, -0.285856)134.5836, -36.8148, -49.7957
4given(0.424223, -0.303003, 0.85336), (0.718396, 0.686323, -0.113437), (-0.551309, 0.661174, 0.50883)73.016, -51.7591, 15.9503

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Components

#1: Protein
PROTEIN (B-POL SUBUNIT OF HEAT-LABILE ENTEROTOXIN) / ETB-POL


Mass: 14293.311 Da / Num. of mol.: 5 / Fragment: SUBUNIT B
Source method: isolated from a genetically manipulated source
Details: THE B SUBUNIT HAS A PEPTIDE WITH ANTI-HSV ACTIVITY AS AN EXTENSION.
Source: (gene. exp.) Escherichia coli (E. coli)
Description: THE PROTEIN WAS CLONED AND EXPRESSED IN VIBRIO CHOLERA
Plasmid: PAM320 / Production host: Vibrio cholerae (bacteria) / References: UniProt: P13811, UniProt: P0CK94*PLUS
Has protein modificationY

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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: 5.54 Å3/Da / Density % sol: 78 %
Crystal growpH: 6 / Details: pH 6
Crystal
*PLUS
Density % sol: 74 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
20.8 Mlithium sulfate1drop
32 %PEG80001drop
40.8 Mlithium sulfate1reservoir
52 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→34.6 Å / Num. obs: 16377 / % possible obs: 74.2 % / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 6.9
Reflection shellResolution: 3.3→3.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.48 / % possible all: 76.7
Reflection
*PLUS
Num. measured all: 64075
Reflection shell
*PLUS
Highest resolution: 3.3 Å / % possible obs: 76.7 % / Num. unique obs: 4728

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
X-PLOR3.84refinement
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1LTR, CHAINS D-H

1ltr


Resolution: 3.3→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.255 620 5 %RANDOM
Rwork0.212 ---
obs0.212 12394 65 %-
Refine analyzeLuzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 3.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 0 0 4186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d17
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : _ / Rms dev position: _ / Weight Biso : _ / Weight position: _

Ens-IDDom-IDNCS model details
11RESTRAINTS
22
33
44
LS refinement shellResolution: 3.3→3.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.32 50 5 %
Rwork0.29 1104 -
obs--63 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.3 Å / σ(F): 3 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg17
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / % reflection Rfree: 5 % / Rfactor Rwork: 0.29

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