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- PDB-1ltr: CRYSTAL STRUCTURE OF THE B SUBUNIT OF HUMAN HEAT-LABILE ENTEROTOX... -

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Basic information

Entry
Database: PDB / ID: 1ltr
TitleCRYSTAL STRUCTURE OF THE B SUBUNIT OF HUMAN HEAT-LABILE ENTEROTOXIN FROM E. COLI CARRYING A PEPTIDE WITH ANTI-HSV ACTIVITY
ComponentsHEAT-LABILE ENTEROTOXIN
KeywordsENTEROTOXIN / 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 / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsMatkovic-Calogovic, D. / Loreggian, 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. / Loregian, 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. / Dauter, Z. / Kingma, J. / Witholt, B. / Hol, W.G.
History
DepositionJul 31, 1998Processing site: BNL
Revision 1.0Feb 9, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: HEAT-LABILE ENTEROTOXIN
E: HEAT-LABILE ENTEROTOXIN
F: HEAT-LABILE ENTEROTOXIN
G: HEAT-LABILE ENTEROTOXIN
H: HEAT-LABILE ENTEROTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,31411
Polymers63,7385
Non-polymers5766
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15580 Å2
ΔGint-158 kcal/mol
Surface area21140 Å2
MethodPISA
2
D: HEAT-LABILE ENTEROTOXIN
E: HEAT-LABILE ENTEROTOXIN
F: HEAT-LABILE ENTEROTOXIN
G: HEAT-LABILE ENTEROTOXIN
H: HEAT-LABILE ENTEROTOXIN
hetero molecules

D: HEAT-LABILE ENTEROTOXIN
E: HEAT-LABILE ENTEROTOXIN
F: HEAT-LABILE ENTEROTOXIN
G: HEAT-LABILE ENTEROTOXIN
H: HEAT-LABILE ENTEROTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,62922
Polymers127,47610
Non-polymers1,15312
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area33130 Å2
ΔGint-322 kcal/mol
Surface area40330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.230, 127.230, 174.190
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(0.420218, 0.720394, -0.55177), (-0.311096, 0.685583, 0.658176), (0.852429, -0.104924, 0.512206)15.1894, 48.4932, -77.1178
2given(-0.511333, 0.858746, -0.033083), (0.225737, 0.171358, 0.958999), (0.829205, 0.4829, -0.281472)97.7006, 25.709, -108.4294
3given(-0.507292, 0.222247, 0.832623), (0.860996, 0.171773, 0.478728), (-0.036627, 0.95974, -0.278493)133.8466, -36.0823, -51.6803
4given(0.427293, -0.308821, 0.849736), (0.723093, 0.680917, -0.116143), (-0.542732, 0.664065, 0.514257)73.5813, -51.7674, 14.3755

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Components

#1: Protein
HEAT-LABILE ENTEROTOXIN / ETB-R2


Mass: 12747.591 Da / Num. of mol.: 5 / Fragment: SUBUNIT B-R2 / Mutation: N103K
Source method: isolated from a genetically manipulated source
Details: THE B SUBUNIT HAS A PEPTIDE WITH ANTI-HSV ACTIVITY AS AN EXTENSION, RESIDUES 104-113
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PAM320 / Production host: Vibrio sp. (bacteria) / Strain (production host): SP60 / References: UniProt: P13811, UniProt: P0CK94*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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 / 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: 77 %
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: 1.4
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Feb 1, 1998 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 3.04→23.19 Å / Num. obs: 27477 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.044 / Net I/σ(I): 11.8
Reflection shellResolution: 3.04→3.39 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 0.1 / % possible all: 95.6
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 23.2 Å / Num. measured all: 97277

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALEFROM CCP4data reduction
AMoREphasing
X-PLOR3.84refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LTS, CHAINS D-H

1lts


Resolution: 3.04→8 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): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1770 7 %RANDOM
Rwork0.1828 ---
obs0.1828 25803 92 %-
Displacement parametersBiso mean: 23 Å2
Refine analyzeLuzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 3.04→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4381 0 30 116 4527
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_d18
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: 3.04→3.17 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2747 193 10.9 %
Rwork0.2786 2706 -
obs--90 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor obs: 0.2786

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