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- PDB-2qn5: Crystal Structure and Functional Study of the Bowman-Birk Inhibit... -

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Basic information

Entry
Database: PDB / ID: 2qn5
TitleCrystal Structure and Functional Study of the Bowman-Birk Inhibitor from Rice Bran in Complex with Bovine Trypsin
Components
  • Bowman-Birk type bran trypsin inhibitor
  • Cationic trypsin
KeywordsHydrolase inhibitor/Hydrolase / RBTI / Bowman-Birk Inhibitor / monocotyledonous plant / reactive-site loop / protease-inhibitor / plant-pest systems / Protease inhibitor / Serine protease inhibitor / Calcium / Digestion / Hydrolase / Metal-binding / Secreted / Zymogen / Hydrolase inhibitor-Hydrolase COMPLEX / HETERO-DIMER
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 / Serine proteases, trypsin family, serine 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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 bran trypsin inhibitor
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLi, H.T. / Lin, Y.H. / Guan, H.H. / Hsieh, Y.C. / Wang, A.H.J. / Chen, C.J.
Citation
Journal: To be Published
Title: Crystal Structure and Functional Study of the Bowman-Birk Inhibitor from Rice Bran in Complex with Bovine Trypsin
Authors: Li, H.T. / Lin, Y.H. / Huang, Y.C. / Guan, H.H. / Hsieh, Y.C. / Chang, T. / Wang, A.H.J. / Chen, C.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Purification, crystallization and preliminary X-ray crystallographic analysis of rice Bowman-Birk inhibitor from Oryza sativa
Authors: Lin, Y.H. / Li, H.T. / Huang, Y.C. / Hsieh, Y.C. / Guan, H.H. / Liu, M.Y. / Chang, T. / Wang, A.H.J. / Chen, C.J.
History
DepositionJul 18, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Bowman-Birk type bran trypsin inhibitor
T: Cationic trypsin


Theoretical massNumber of molelcules
Total (without water)38,4212
Polymers38,4212
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.653, 69.653, 158.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Bowman-Birk type bran trypsin inhibitor / Protein RBBI3-3 / RBTI / OSE727A


Mass: 15096.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryza sativa (Asian cultivated rice) / Strain: japonica cultivar-group / References: UniProt: Q0JR25
#2: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 11% PEG6000, 0.1M HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2006
Details: Vertically Collimating Vertically Collimating Premirror, Fixed-Exit Double Crystal, Si(111) Monochromator, Toroidal Focusing Mirror
RadiationMonochromator: Fixed-Exit Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→30 Å / Num. obs: 11039 / % possible obs: 98.9 % / Redundancy: 10.6 % / Rsym value: 0.056 / Net I/σ(I): 36.1
Reflection shellResolution: 2.72→2.82 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 3.85 / Num. unique all: 1043 / Rsym value: 0.593 / % possible all: 95.8

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Processing

Software
NameVersionClassification
Blu-IceControl Softwaredata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ABC and 1C2A

1abc

1c2a


Resolution: 3→30 Å / Isotropic thermal model: anisotropic / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.322 848 -RANDOM
Rwork0.2562 ---
all-8332 --
obs-8163 98 %-
Displacement parametersBiso mean: 2.425 Å2
Baniso -1Baniso -2Baniso -3
1--13.829 Å20 Å20 Å2
2---13.829 Å20 Å2
3---27.658 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 0 137 2620
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0084
X-RAY DIFFRACTIONc_angle_deg1.6274
X-RAY DIFFRACTIONc_dihedral_angle_d24.9358
X-RAY DIFFRACTIONc_improper_angle_d1.1333
LS refinement shellResolution: 3→3.11 Å
RfactorNum. reflection% reflection
Rfree0.4233 70 -
Rwork0.3354 --
obs-778 96.5 %

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