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- PDB-1k9b: Crystal structure of the bifunctional soybean Bowman-Birk inhibit... -

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Entry
Database: PDB / ID: 1k9b
TitleCrystal structure of the bifunctional soybean Bowman-Birk inhibitor at 0.28 nm resolution. Structural peculiarities in a folded protein conformation
ComponentsBOWMAN-BIRK TYPE PROTEINASE INHIBITOR
KeywordsHYDROLASE INHIBITOR / TRIPPLE-STRANDED BETA HAIRPIN / DOUBLE-HEADED
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
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVoss, R.H. / Ermler, U. / Essen, L.O. / Wenzl, G. / Kim, Y.M. / Flecker, P.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Crystal Structure of Cancer Chemopreventive Bowman-Birk Inhibitor in Ternary Complex with Bovine Trypsin at 2.3 Ao Resolution. Structural Basis of Janus-faced Serine Protease Inhibitor Specificity
Authors: Koepke, J. / Ermler, U. / Warkentin, E. / Wenzl, G. / 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: 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. / Duerr, I. / Wenzl, G. / Vogt, M. / Flecker, P.
#4: Journal: Eur.J.Biochem. / Year: 1995
Title: Template-directed protein folding into a metastable state of increased activity
Authors: Flecker, P.
#5: 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.
History
DepositionOct 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.classification / _software.name
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BOWMAN-BIRK TYPE PROTEINASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)6,4321
Polymers6,4321
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.1, 86.1, 86.1
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Cell settingtetragonal
Space group name H-MP4132

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Components

#1: Protein BOWMAN-BIRK TYPE PROTEINASE INHIBITOR / BBI


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


Mass: 18.015 Da / Num. of mol.: 17 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: PEG 4000, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, SITTING DROP at 289K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.04 Å
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: 2.5→60.9 Å / Num. all: 3891 / Num. obs: 26756 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 6.88 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058
Reflection shellResolution: 2.8→3 Å / Rmerge(I) obs: 0.3 / % possible all: 70

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Processing

Software
NameVersionClassification
WEISdata scaling
ROTAVATAdata reduction
X-PLORmodel building
X-PLOR3.1refinement
WEISdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PI2

1pi2


Resolution: 2.8→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.308 272 11.1 %random
Rwork0.221 ---
all-2722 --
obs-2450 96.3 %-
Displacement parametersBiso mean: 28.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.035 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms513 0 0 17 530
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d29.7
X-RAY DIFFRACTIONx_improper_angle_d2.8

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