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- PDB-1tab: STRUCTURE OF THE TRYPSIN-BINDING DOMAIN OF BOWMAN-BIRK TYPE PROTE... -

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Basic information

Entry
Database: PDB / ID: 1tab
TitleSTRUCTURE OF THE TRYPSIN-BINDING DOMAIN OF BOWMAN-BIRK TYPE PROTEASE INHIBITOR AND ITS INTERACTION WITH TRYPSIN
Components
  • BOWMAN-BIRK TYPE PROTEINASE INHIBITOR
  • TRYPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family ...Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease 1 / Bowman-Birk type proteinase inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsTsunogae, Y. / Tanaka, I. / Yamane, T. / Kikkawa, J.-I. / Ashida, T. / Ishikawa, C. / Watanabe, K. / Nakamura, S. / Takahashi, K.
Citation
Journal: J.Biochem.(Tokyo) / Year: 1986
Title: Structure of the trypsin-binding domain of Bowman-Birk type protease inhibitor and its interaction with trypsin.
Authors: Tsunogae, Y. / Tanaka, I. / Yamane, T. / Kikkawa, J. / Ashida, T. / Ishikawa, C. / Watanabe, K. / Nakamura, S. / Takahashi, K.
#1: Journal: J.Biochem.(Tokyo) / Year: 1987
Title: The Structure of Bowman-Birk Type Protease Inhibitor A-II from Peanut (Arachis Hypogaea) at 3.3 Angstroms Resolution
Authors: Suzuki, A. / Tsunogae, Y. / Tanaka, I. / Yamane, T. / Ashida, T. / Norioka, S. / Hara, S. / Ikenaka, T.
History
DepositionOct 15, 1990Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: TRYPSIN
I: BOWMAN-BIRK TYPE PROTEINASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)32,4662
Polymers32,4662
Non-polymers00
Water2,522140
1
E: TRYPSIN
I: BOWMAN-BIRK TYPE PROTEINASE INHIBITOR

E: TRYPSIN
I: BOWMAN-BIRK TYPE PROTEINASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)64,9334
Polymers64,9334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_646y+1,x-1,-z+11
Unit cell
Length a, b, c (Å)55.420, 55.420, 181.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: PRO I 29 AND PRO I 71 ARE CIS PROLINES.

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Components

#1: Protein TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: PANCREAS / References: UniProt: P00760, trypsin
#2: Protein BOWMAN-BIRK TYPE PROTEINASE INHIBITOR


Mass: 9142.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P01058
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal grow
*PLUS
Temperature: unknown K / pH: 6.5 / Method: microdialysis / Details: took 3 from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1buttom
22 M1buttomNaCl
30.05 Msodium cacodylate1buttom
42 M1reservoirNaCl
50.05 Msodium cacodylate1reservoir
612 %(w/v)ammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.2 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 0 140 2044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.027
X-RAY DIFFRACTIONp_angle_d0.054
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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