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- PDB-1lts: REFINED STRUCTURE OF E. COLI HEAT LABILE ENTEROTOXIN, A CLOSE REL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lts | ||||||
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Title | REFINED STRUCTURE OF E. COLI HEAT LABILE ENTEROTOXIN, A CLOSE RELATIVE OF CHOLERA TOXIN | ||||||
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![]() | TOXIN | ||||||
Function / homology | ![]() toxin activity / killing of cells of another organism / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Sixma, T.K. / Hol, W.G.J. | ||||||
![]() | ![]() Title: Refined structure of Escherichia coli heat-labile enterotoxin, a close relative of cholera toxin. Authors: Sixma, T.K. / Van Zanten, B.A.M. / Dauter, Z. / Hol, W.G.J. #1: ![]() Title: Lactose Binding to Heat-Labile Enterotoxin Revealed by X-Ray Crystallography Authors: Sixma, T.K. / Pronk, S.E. / Kalk, K.H. / Van Zanten, B.A.M. / Berghuis, A.M. / Hol, W.G.J. #2: ![]() Title: Crystal Structure of a Cholera Toxin-Related Heat-Labile Enterotoxin from E. Coli Authors: Sixma, T.K. / Pronk, S.E. / Kalk, K.H. / Wartna, E.S. / Van Zanten, B.A.M. / Witholt, B. / Hol, W.G.J. #3: ![]() Year: 1991 Title: Native Non-Isomorphism in the Structure Determination of Heat Labile Enterotoxin (Lt) from E. Coli Authors: Sixma, T.K. / Pronk, S.E. / Van Scheltinga, A.C.T. / Aguirre, A. / Kalk, K.H. / Vriend, G. / Hol, W.G.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.4 KB | Display | ![]() |
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PDB format | ![]() | 129.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.4 KB | Display | ![]() |
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Full document | ![]() | 478.8 KB | Display | |
Data in XML | ![]() | 31.6 KB | Display | |
Data in CIF | ![]() | 44.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO D 93 / 2: CIS PROLINE - PRO E 93 / 3: CIS PROLINE - PRO F 93 / 4: CIS PROLINE - PRO G 93 / 5: CIS PROLINE - PRO H 93 / 6: CIS PROLINE - PRO A 178 | ||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | ROTATION MATRICES HAVE BEEN INCLUDED FOR PARTIAL NON-CRYSTALLOGRAPHIC FIVEFOLD SYMMETRY OF THE B SUBUNITS. ROTATIONS ACT ON CARTESIAN COORDINATES, WITH THE ORIGIN AS CENTER OF ROTATION (NO TRANSLATION ALONG THE FIVEFOLD AXIS). RMS DEVIATION FOR ALL 515 ALPHA CARBONS OF THE B SUBUNIT IS 0.6 ANGSTROMS. (SUPERPOSITION OF INDIVIDUAL B SUBUNITS GIVES BETTER VALUES OF 0.20 - 0.45 ANGSTROMS). ROTATIONS INCLUDED IN MTRIX CARDS RELATE B-PENTAMERS VIA FIVEFOLD AXIS: KAPPA PHI PSI RELATING 288.0 0.4 96.0 B1 TO B2 (MTRIX1) 216.0 0.4 96.0 B1 TO B3 (MTRIX2) 144.0 0.4 96.0 B1 TO B4 (MTRIX3) 72.0 0.4 96.0 B1 TO B5 (MTRIX4) THE TRANSFORMATION PRESENTED AS *MTRIX 1* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *E* WHEN APPLIED TO CHAIN *D*. THE TRANSFORMATION PRESENTED AS *MTRIX 2* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *F* WHEN APPLIED TO CHAIN *D*. THE TRANSFORMATION PRESENTED AS *MTRIX 3* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *G* WHEN APPLIED TO CHAIN *D*. THE TRANSFORMATION PRESENTED AS *MTRIX 4* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *H* WHEN APPLIED TO CHAIN *D*. |
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Components
#1: Protein | Mass: 11807.539 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 21354.600 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein/peptide | | Mass: 4953.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Water | ChemComp-HOH / | Compound details | THIS IS THE UNNICKED AND UNREDUCED FORM OF THE TOXIN. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.62 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: microdialysisDetails: two-layer method, taken from Pronk, S.E. et al (1985). J. Biol. Chem., 260, 13580-13584. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.95 Å / Lowest resolution: 9999 Å / Num. obs: 53762 / % possible obs: 94.4 % / Num. measured all: 230816 / Rmerge(I) obs: 0.088 |
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Processing
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Refinement | Resolution: 1.95→8 Å / σ(F): 0 Details: MEAN TEMPERATURE FACTORS ARE HIGH. (SEE SUBUNIT NUMBERING SCHEME, REMARK 10).
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Refinement step | Cycle: LAST / Resolution: 1.95→8 Å
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Refinement | *PLUS Highest resolution: 1.95 Å / Lowest resolution: 8 Å / Num. reflection all: 52397 / σ(F): 0 / Rfactor all: 0.182 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS Biso mean: 33 Å2 | |||||||||||||||
Refine LS restraints | *PLUS
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