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- PDB-2fj8: High resolution structure of barley Bowman-Birk inhibitor -

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Basic information

Entry
Database: PDB / ID: 2fj8
TitleHigh resolution structure of barley Bowman-Birk inhibitor
ComponentsBowman-Birk type trypsin inhibitor
KeywordsHydrolase Inhibitor / all-beta
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 trypsin inhibitor
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsSong, H.K.
CitationJournal: To be Published
Title: High resolution structure of barley Bowman-Birk inhibitor
Authors: Song, H.K.
History
DepositionJan 2, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bowman-Birk type trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)13,9321
Polymers13,9321
Non-polymers00
Water6,143341
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.342, 62.342, 95.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-177-

HOH

21A-438-

HOH

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Components

#1: Protein Bowman-Birk type trypsin inhibitor / BBBI


Mass: 13932.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / Tissue: seeds / References: UniProt: P12940
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.64
Details: PEG3000, pH 5.64, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 24, 2005
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.19→50 Å / Num. obs: 58682 / % possible obs: 96.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.19→1.23 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 0.881 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24407 2968 5.1 %RANDOM
Rwork0.2111 ---
obs0.21284 55768 96.6 %-
all-58682 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.228 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.045 Å0.044 Å
Refinement stepCycle: LAST / Resolution: 1.19→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 0 341 1259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022952
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9951299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5475119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.63221.17634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19915161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4061512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02718
X-RAY DIFFRACTIONr_nbd_refined0.1920.2450
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2642
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.233
X-RAY DIFFRACTIONr_mcbond_it1.4441.5630
X-RAY DIFFRACTIONr_mcangle_it2.17721011
X-RAY DIFFRACTIONr_scbond_it4.2323363
X-RAY DIFFRACTIONr_scangle_it4.1794.5288
X-RAY DIFFRACTIONr_rigid_bond_restr3.8683993
X-RAY DIFFRACTIONr_sphericity_free3.7813341
X-RAY DIFFRACTIONr_sphericity_bonded4.4273918
LS refinement shellResolution: 1.19→1.221 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 255 -
Rwork0.172 4158 -
obs--99.98 %

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