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- PDB-1avu: TRYPSIN INHIBITOR FROM SOYBEAN (STI) -

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Basic information

Entry
Database: PDB / ID: 1avu
TitleTRYPSIN INHIBITOR FROM SOYBEAN (STI)
ComponentsTRYPSIN INHIBITOR
KeywordsSERINE PROTEASE INHIBITOR / TRYPSIN INHIBITOR / KUNITZ-TYPE / BETA-TREFOIL FOLD
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
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSong, H.K. / Suh, S.W.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Kunitz-type soybean trypsin inhibitor revisited: refined structure of its complex with porcine trypsin reveals an insight into the interaction between a homologous inhibitor from Erythrina ...Title: Kunitz-type soybean trypsin inhibitor revisited: refined structure of its complex with porcine trypsin reveals an insight into the interaction between a homologous inhibitor from Erythrina caffra and tissue-type plasminogen activator.
Authors: Song, H.K. / Suh, S.W.
#1: Journal: Thesis, Seoul National University / Year: 1997
Title: Crystal Structure Analyses of Human A1-Antitrypsin, Soybean Kunitz-Type Trypsin Inhibitor, and Barley Chitinase
Authors: Song, H.K.
#2: Journal: Mol.Cells / Year: 1993
Title: Crystallization of Kunitz-Type Soybean Trypsin Inhibitor
Authors: Lee, J.K. / Song, H.K. / Hwang, K.Y. / Kim, K.K. / Suh, S.W.
#3: Journal: Thesis, Seoul National University / Year: 1993
Title: Crystallization and Preliminary X-Ray Crystallographic Study of Kunitz-Type Soybean Trypsin Inhibitor
Authors: Lee, J.K.
History
DepositionSep 20, 1997Processing site: BNL
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 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

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Assembly

Deposited unit
A: TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)20,1161
Polymers20,1161
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.420, 58.080, 96.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRYPSIN INHIBITOR / STI


Mass: 20115.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / Organ: SEED / References: UniProt: P01070
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.75 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: other / Details: Lee, J., (1993) Mol. Cells, 3, 335.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Mar 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. obs: 10234 / % possible obs: 76 % / Observed criterion σ(I): 0.5 / Redundancy: 2.7 % / Rmerge(I) obs: 0.045
Reflection shellResolution: 2.1→2.3 Å / % possible all: 26.7
Reflection
*PLUS
Lowest resolution: 33 Å / Num. measured all: 27868
Reflection shell
*PLUS
% possible obs: 26.7 %

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Processing

Software
NameVersionClassification
PROCORdata collection
FSSCALINGdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
PROCORdata reduction
FSSCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TIE

1tie


Resolution: 2.3→8 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -10 %RANDOM
Rwork0.198 ---
obs0.198 9079 --
Displacement parametersBiso mean: 38.3 Å2
Refine analyzeLuzzati d res low obs: 0 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 0 44 1325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.4
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19X.PRO
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3
X-RAY DIFFRACTION4

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