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- PDB-1e9t: High resolution solution structure of human intestinal trefoil factor -

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Basic information

Entry
Database: PDB / ID: 1e9t
TitleHigh resolution solution structure of human intestinal trefoil factor
ComponentsINTESTINAL TREFOIL FACTOR
KeywordsCELL MOTILITY FACTOR / INTESTINAL TREFOIL FACTOR / SOLUTION STRUCTURE / TREFOIL DOMAIN / NMR SPECTROSCOPY
Function / homology
Function and homology information


maintenance of gastrointestinal epithelium / regulation of glucose metabolic process / secretory granule / Estrogen-dependent gene expression / extracellular space / extracellular region / identical protein binding
Similarity search - Function
P-type trefoil, chordata / Spasmolytic Protein, domain 1 / Spasmolytic Protein; domain 1 / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain ...P-type trefoil, chordata / Spasmolytic Protein, domain 1 / Spasmolytic Protein; domain 1 / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS
AuthorsLemercinier, X. / Muskett, F. / Cheeseman, B. / McIntosh, P. / Carr, M.
CitationJournal: Biochemistry / Year: 2001
Title: High-Resolution Solution Structure of Human Intestinal Trefoil Factor and Functional Insights from Detailed Structural Comparisons with the Other Members of the Trefoil Family of Mammalian Cell Motility Factors
Authors: Lemercinier, X. / Muskett, F.W. / Cheeseman, B. / Mcintosh, P.B. / Thim, L. / Carr, M.D.
History
DepositionOct 26, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Other
Revision 1.2Jan 15, 2020Group: Other / Category: pdbx_database_status
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conn.pdbx_dist_value
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: SEQUENTIAL AND MEDIUM-RANGE NOE PATTERN, AND KABSCH AND SANDER ... HELIX DETERMINATION METHOD: SEQUENTIAL AND MEDIUM-RANGE NOE PATTERN, AND KABSCH AND SANDER ALGORITHM IN MOLMOL
Remark 700 SHEET DETERMINATION METHOD: PATTERN OF SEQUENTIAL AND LONG-RANGE NOES

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTESTINAL TREFOIL FACTOR


Theoretical massNumber of molelcules
Total (without water)6,5871
Polymers6,5871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)85 / 100CONSISTENCY WITH THE NMR STRUCTURAL DATA
RepresentativeModel #1

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Components

#1: Protein INTESTINAL TREFOIL FACTOR / HITF


Mass: 6587.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: RECOMBINANT HITF PRODUCED IN A YEAST EXPRESSION VECTOR.
Plasmid: PHW 1066 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): MT-663 / References: UniProt: Q07654
Compound detailsTHE PROTEIN CONTAINS A 21 RESIDUE SIGNAL SEQUENCE MAY HAVE A ROLE IN PROMOTING CELL MIGRATION.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121ROESY
131TOCSY AND DQF-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED FROM 2D 1H NMR DATA ACQUIRED FROM SAMPLES OF HITF

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Sample preparation

Sample conditionsIonic strength: 25 MM POTASSIUM PHOSPHATE AND 100 MM POTASSIUM CHLORIDE
pH: 6 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Varian UNITYPLUSVarianUNITYPLUS5002

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Processing

NMR software
NameDeveloperClassification
DYANAGUNTERT,WUTHRICHrefinement
XEASYstructure solution
DYANAstructure solution
RefinementMethod: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: AFTER THE FINAL DYANA CALCULATIONS, 85 SATISFACTORILY CONVERGED HITF STRUCTURES WERE OBTAINED FROM 100 RANDOM STARTING CONFORMATIONS. THE CONVERGED STRUCTURES CONTAIN NO DISTANCE CONSTRAINT ...Details: AFTER THE FINAL DYANA CALCULATIONS, 85 SATISFACTORILY CONVERGED HITF STRUCTURES WERE OBTAINED FROM 100 RANDOM STARTING CONFORMATIONS. THE CONVERGED STRUCTURES CONTAIN NO DISTANCE CONSTRAINT OR VAN DER WAALS VIOLATIONS GREATER THAN 0.5 A AND NO DIHEDRAL ANGLE VIOLATIONS GREATER THAN 5 DEGREES, WITH AN AVERAGE VALUE FOR THE DYANA TARGET FUNCTION OF 4.33.
NMR ensembleConformer selection criteria: CONSISTENCY WITH THE NMR STRUCTURAL DATA
Conformers calculated total number: 100 / Conformers submitted total number: 85

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