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- PDB-1pi2: REACTIVE SITES OF AN ANTICARCINOGENIC BOWMAN-BIRK PROTEINASE INHI... -

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Basic information

Entry
Database: PDB / ID: 1pi2
TitleREACTIVE SITES OF AN ANTICARCINOGENIC BOWMAN-BIRK PROTEINASE INHIBITOR ARE SIMILAR TO OTHER TRYPSIN INHIBITORS
ComponentsBOWMAN-BIRK INHIBITOR (PI-II)
KeywordsSERINE PROTEINASE INHIBITOR
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Cysteine Protease (Bromelain) Inhibitor, subunit H / Cysteine Protease (Bromelain) Inhibitor, subunit H / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Bowman-Birk type proteinase inhibitor D-II
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsChen, P. / Rose, J. / Wang, B.C.
Citation
Journal: J.Biol.Chem. / Year: 1992
Title: Reactive sites of an anticarcinogenic Bowman-Birk proteinase inhibitor are similar to other trypsin inhibitors.
Authors: Chen, P. / Rose, J. / Love, R. / Wei, C.H. / Wang, B.C.
#1: Journal: J.Biol.Chem. / Year: 1983
Title: Crystallization of Two Cubic Forms of Soybean Trypsin Inhibitor E-I, a Member of the Bowman-Birk Inhibitor Family
Authors: Wei, C.H.
History
DepositionMar 26, 1991Processing site: BNL
Revision 1.0Apr 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 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
A: BOWMAN-BIRK INHIBITOR (PI-II)


Theoretical massNumber of molelcules
Total (without water)7,2131
Polymers7,2131
Non-polymers00
Water00
1
A: BOWMAN-BIRK INHIBITOR (PI-II)
x 6


Theoretical massNumber of molelcules
Total (without water)43,2806
Polymers43,2806
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_555-x+3/4,-z+3/4,-y+3/41
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation22_564z+1/4,-y+5/4,x-1/41
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
Unit cell
Length a, b, c (Å)89.960, 89.960, 89.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Atom site foot note1: RESIDUES 18 AND 44 ARE CIS-PROLINES.

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Components

#1: Protein BOWMAN-BIRK INHIBITOR (PI-II)


Mass: 7213.337 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / References: UniProt: P01064
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: 4.2 Å3/Da / Density % sol: 70.73 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 4.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 Msoium acetate-acetic acid1drop
20.03 mg/mlprotein1drop
30.2 %sodium chloride1drop
41.8 %(w/v)PEG40001drop
50.09 %sodium azide1drop
740 %satammonium sulfate1reservoir
6ammonium sulfate1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 9999 Å / Num. all: 5488 / % possible obs: 95.1 % / Num. measured all: 75913 / Rmerge(I) obs: 0.0777

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Processing

SoftwareName: GPRLSA / Classification: refinement
RefinementRfactor obs: 0.236 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms461 0 0 0 461
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.8
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
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor obs: 0.236 / Lowest resolution: 8 Å / Num. reflection obs: 3287
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_bond_d0.021

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