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- PDB-1d6r: CRYSTAL STRUCTURE OF CANCER CHEMOPREVENTIVE BOWMAN-BIRK INHIBITOR... -

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Basic information

Entry
Database: PDB / ID: 1d6r
TitleCRYSTAL STRUCTURE OF CANCER CHEMOPREVENTIVE BOWMAN-BIRK INHIBITOR IN TERNARY COMPLEX WITH BOVINE TRYPSIN AT 2.3 A RESOLUTION. STRUCTURAL BASIS OF JANUS-FACED SERINE PROTEASE INHIBITOR SPECIFICITY
Components
  • BOWMAN-BIRK PROTEINASE INHIBITOR PRECURSOR
  • TRYPSINOGEN
KeywordsHYDROLASE / PROTEASE INHIBITOR / SERINE PROTEASE / BOWMAN-BIRK INHIBITOR
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
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 / Serine proteases, trypsin family, histidine active site ...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 / 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)
Glycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsKoepke, J. / Ermler, U. / Wenzl, G. / Flecker, P.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of cancer chemopreventive Bowman-Birk inhibitor in ternary complex with bovine trypsin at 2.3 A resolution. Structural basis of Janus-faced serine protease inhibitor specificity.
Authors: Koepke, J. / Ermler, U. / Warkentin, E. / Wenzl, G. / Flecker, P.
#1: Journal: Eur.J.Biochem. / Year: 1996
Title: Crystal structure of the bifunctional soybean Bowman-Birk inhibitor at 0.28-nm resolution-structural peculiarities in a folded protein conformation.
Authors: Voss, R.H. / Ermler, U. / Essen, L.O. / Wenzl, G. / Kim, Y.M. / Flecker, P.
#2: Journal: Eur.J.Biochem. / Year: 1987
Title: Chemical synthesis, molecular cloning and expression of gene coding for a Bowman-Birk-type proteinase inhibitor
Authors: Flecker, P.
#3: Journal: J.Biochem.Biophys.Methods / Year: 1996
Title: Proteolytic cleavage of soybean Bowman-Birk inhibitor monitored by means of high-performance capillary electrophoresis
Authors: Jensen, B. / Unger, K.K. / Uebe, J. / Gey, M. / Kim, Y.M. / Flecker, P.
#4: Journal: FEBS Lett. / Year: 1989
Title: A new and general procedure for refolding mutant Bowman-Birk-type proteinase inhibitors on trypsin-Sepharose as a matrix with complementary structure
Authors: Flecker, P.
#5: Journal: Eur.J.Biochem. / Year: 1995
Title: Template-directed protein folding into a metastable state of increased activity
Authors: Flecker, P.
#6: Journal: Eur.J.Biochem. / Year: 1998
Title: Mutational analysis of disulfide bonds in the trypsin-reactive subdomain of a Bowman-Birk-type inhibitor of trypsin and chymotrypsin. Cooperative versus autonomous refolding of subdomains.
Authors: Philipp, S. / Kim, Y.M. / Durr, I. / Wenzl, G. / Vogt, M. / Flecker, P.
History
DepositionOct 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: TRYPSINOGEN
I: BOWMAN-BIRK PROTEINASE INHIBITOR PRECURSOR


Theoretical massNumber of molelcules
Total (without water)29,7562
Polymers29,7562
Non-polymers00
Water2,090116
1
A: TRYPSINOGEN
I: BOWMAN-BIRK PROTEINASE INHIBITOR PRECURSOR

A: TRYPSINOGEN
I: BOWMAN-BIRK PROTEINASE INHIBITOR PRECURSOR


Theoretical massNumber of molelcules
Total (without water)59,5124
Polymers59,5124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_647y+1,x-1,-z+21
Unit cell
Length a, b, c (Å)55.600, 55.600, 183.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein TRYPSINOGEN


Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: CATIONIC PRECURSOR / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cell: ACINAR CELL / Organ: PANCREAS / References: UniProt: P00760, trypsin
#2: Protein BOWMAN-BIRK PROTEINASE INHIBITOR PRECURSOR


Mass: 6431.538 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / References: UniProt: P01055
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTRIPLE-STRANDED B-HAIRPIN MOTIF OF BOWMAN-BIRK PROTEASE INHIBITOR INTERACTS WITH SURFACE LOOPS ...TRIPLE-STRANDED B-HAIRPIN MOTIF OF BOWMAN-BIRK PROTEASE INHIBITOR INTERACTS WITH SURFACE LOOPS SURROUNDING THE ACTIVE SITE OF BOVINE TRYPSIN IN AN UNPRECEDENT MANNER.
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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PROTEIN SOLUTION: TRIS/CL, CACL2, MGSO4.7H2O, NAN3 PLUS PRECIPITANT PRECIPITANTS: (NH4)2SO4, MDP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 mMprotein11
212.5 %satammonium sulfate11
325 mMTris-HCl11
410 mM11CaCl2
50.55 M11MgSO4(7H2O)
61.6 %(v/v)MDP11
70.08 %(w/v)11NaN3
837.5 %satammonium sulfate12

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.04
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Apr 5, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. all: 54604 / Num. obs: 54604 / % possible obs: 82.3 % / Observed criterion σ(F): 0.01 / Observed criterion σ(I): 0.01 / Redundancy: 4.838 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.3→2.4 Å / % possible all: 60.9
Reflection
*PLUS
Num. obs: 18001 / Num. measured all: 54604
Reflection shell
*PLUS
% possible obs: 60.9 %

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Processing

Software
NameVersionClassification
WEISdata scaling
ROTAVATAdata reduction
X-PLOR3.1refinement
WEISdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.3→8 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 564 -RANDOM
Rwork0.152 ---
all0.152 18001 --
obs0.152 11286 82.3 %-
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 0 116 2172
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.194
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.262
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.905
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.262
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.905

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