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- PDB-1ba7: SOYBEAN TRYPSIN INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1ba7
TitleSOYBEAN TRYPSIN INHIBITOR
ComponentsTRYPSIN INHIBITOR (KUNITZ)
KeywordsSERINE PROTEASE INHIBITOR / TRYPSIN INHIBITOR (KUNITZ)
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: 2.5 Å
AuthorsDe Meester, P. / Brick, P. / Lloyd, L.F. / Blow, D.M. / Onesti, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of the Kunitz-type soybean trypsin inhibitor (STI): implication for the interactions between members of the STI family and tissue-plasminogen activator.
Authors: De Meester, P. / Brick, P. / Lloyd, L.F. / Blow, D.M. / Onesti, S.
#1: 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.
#2: Journal: Biochemistry / Year: 1974
Title: Crystal Structure of the Complex of Porcine Trypsin with Soybean Trypsin Inhibitor (Kunitz) at 2.6-A Resolution
Authors: Sweet, R.M. / Wright, H.T. / Janin, J. / Chothia, C.H. / Blow, D.M.
History
DepositionApr 22, 1998Processing site: BNL
Revision 1.0Jun 17, 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 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN INHIBITOR (KUNITZ)
B: TRYPSIN INHIBITOR (KUNITZ)


Theoretical massNumber of molelcules
Total (without water)40,2312
Polymers40,2312
Non-polymers00
Water2,828157
1
A: TRYPSIN INHIBITOR (KUNITZ)


Theoretical massNumber of molelcules
Total (without water)20,1161
Polymers20,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRYPSIN INHIBITOR (KUNITZ)


Theoretical massNumber of molelcules
Total (without water)20,1161
Polymers20,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.110, 53.870, 58.200
Angle α, β, γ (deg.)71.75, 90.00, 82.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TRYPSIN INHIBITOR (KUNITZ)


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


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SCISSILE BOND IS BETWEEN ARG 62 AND ILE 63.
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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
21.4 Mphosphate1reservoir
32.5 %(v/v)dioxane1reservoir
41.25 %(v/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Sep 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 14369 / % possible obs: 93.7 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 9.5
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 6.1 / Rsym value: 0.181 / % possible all: 88.6
Reflection shell
*PLUS
% possible obs: 88.6 % / Num. unique obs: 1914

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Processing

Software
NameVersionClassification
MADNESdata collection
CCP4data reduction
X-PLOR3.851model building
X-PLOR3.851refinement
MADNESdata reduction
CCP4data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TIE

1tie


Resolution: 2.5→15 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION USED
RfactorNum. reflection% reflectionSelection details
Rfree0.223 700 5 %RANDOM
Rwork0.16 ---
obs0.16 14619 94.9 %-
Displacement parametersBiso mean: 36 Å2
Refine analyzeLuzzati d res low obs: 15 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 0 157 2653
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.42
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.68
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.291.5
X-RAY DIFFRACTIONx_mcangle_it5.352
X-RAY DIFFRACTIONx_scbond_it5.382
X-RAY DIFFRACTIONx_scangle_it8.232.5
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.293 96 5 %
Rwork0.282 1653 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.68
LS refinement shell
*PLUS
Rfactor obs: 0.282

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