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- PDB-1tie: CRYSTAL STRUCTURE OF A KUNITZ-TYPE TRYPSIN INHIBITOR FROM ERYTHRI... -

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Basic information

Entry
Database: PDB / ID: 1tie
TitleCRYSTAL STRUCTURE OF A KUNITZ-TYPE TRYPSIN INHIBITOR FROM ERYTHRINA CAFFRA SEEDS
ComponentsERYTHRINA TRYPSIN INHIBITOR
KeywordsPROTEINASE INHIBITOR (TRYPSIN)
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Trypsin inhibitor DE-3
Similarity search - Component
Biological speciesErythrina caffra (lucky beantree)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsOnesti, S. / Brick, P. / Blow, D.M.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Crystal structure of a Kunitz-type trypsin inhibitor from Erythrina caffra seeds.
Authors: Onesti, S. / Brick, P. / Blow, D.M.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallization and Preliminary Diffraction Studies of Erythrina Trypsin Inhibitor
Authors: Onesti, S. / Lloyd, L.F. / Brick, P. / Blow, D.M.
History
DepositionFeb 14, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 700SHEET ETI CONSISTS OF 12 ANTIPARALLEL BETA-STRANDS JOINED BY LONG LOOPS. SIX OF THE STRANDS FORM A ...SHEET ETI CONSISTS OF 12 ANTIPARALLEL BETA-STRANDS JOINED BY LONG LOOPS. SIX OF THE STRANDS FORM A SHORT BARREL WHICH IS CLOSED AT ONE END BY A "LID" CONSISTING OF THE OTHER SIX STRANDS COUPLED IN THREE PAIRS. THE MOLECULE SHOWS APPROXIMATE THREE-FOLD SYMMETRY ABOUT THE THE AXIS OF THE BARREL, WITH THE REPEATING UNIT CONSISTING OF FOUR SEQUENTIAL BETA-STRANDS AND THE CONNECTING LOOPS. THE SHEET PRESENTED AS *B1* ON SHEET RECORDS BELOW IS ACTUALLY THE SIX-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ERYTHRINA TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)19,2971
Polymers19,2971
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.400, 73.400, 143.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein ERYTHRINA TRYPSIN INHIBITOR


Mass: 19296.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erythrina caffra (lucky beantree) / References: UniProt: P09943
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 3.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMacetate1drop
3150 mM1dropNaCl
4distilled water1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 7770 / % possible obs: 93.6 % / Num. measured all: 33533 / Rmerge(I) obs: 0.065

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.5→10 Å /
RfactorNum. reflection
Rwork0.208 -
obs-7770
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 0 61 1293
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg
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
Refinement
*PLUS
Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.64 Å / Total num. of bins used: 10 / Rfactor obs: 0.297

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