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- PDB-2r33: Crystal structure of a Bowman-Birk inhibitor from Vigna unguicula... -

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Basic information

Entry
Database: PDB / ID: 2r33
TitleCrystal structure of a Bowman-Birk inhibitor from Vigna unguiculata seeds
ComponentsBowman-Birk type seed trypsin and chymotrypsin inhibitor
KeywordsPLANT PROTEIN / BOWMAN-BIRK PROTEASE INHIBITOR / VIGNA UNGUICULATA / PLANT-PIS / PROTEIN-PROTEIN INTERACTIONS / Serine protease 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
Biological speciesVigna unguiculata (cowpea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRao, K.N. / Suresh, C.G.
CitationJournal: Biochim.Biophys.Acta / Year: 2007
Title: Bowman-Birk protease inhibitor from the seeds of Vigna unguiculata forms a highly stable dimeric structure.
Authors: Rao, K.N. / Suresh, C.G.
History
DepositionAug 28, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionNov 27, 2007ID: 2OT6
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: 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
Remark 999SEQUENCE The sequence of this inhibitor matching its molecular weight 8.1 kDa was determined using ...SEQUENCE The sequence of this inhibitor matching its molecular weight 8.1 kDa was determined using partial N-terminal sequencing and with the help of electron density map combined with sequences of isoinhibitors reported previously from the same source and considering the possible cleavage at C-terminal. The sequence here differs with the P17734 entry in the Swissprot database in amino acid positions 20, 23, 33, 50, 60 and 62 as clearly seen from the electron density map. Also, IN THE N-TERMINAL ABOUT 16 RESIDUES are missing and in the C-terminal beyond residue 74 is possibly cleaved, as inferred from electron density map and molecular weight. Thus, we believe that the inhibitor whose structure reported here is a modified isoform of the deposited sequence P17734.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bowman-Birk type seed trypsin and chymotrypsin inhibitor
B: Bowman-Birk type seed trypsin and chymotrypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)16,0062
Polymers16,0062
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.510, 61.430, 32.990
Angle α, β, γ (deg.)90.00, 114.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bowman-Birk type seed trypsin and chymotrypsin inhibitor / BTCI


Mass: 8003.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna unguiculata (cowpea) / References: UniProt: Q4VVG2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.87 Å3/Da / Density % sol: 34.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 30% SATURATED AMMONIUM SULFATE 0.1M CITRATE-PHOSPHATE, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 4072 / % possible obs: 99 % / Observed criterion σ(I): 3 / Biso Wilson estimate: 51.9 Å2 / Rsym value: 0.083 / Net I/σ(I): 13.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5.8 / % possible all: 94.7

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC3.4refinement
MOSFLMdata reduction
SCALEITdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: X-RAY COORDINATES OF BOWMAN-BIRK INHIBITOR FROM ADZUKI BEAN

Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Details: RESOLUTION-DEPENDENT WEIGHTING
RfactorNum. reflection% reflectionSelection details
Rfree0.258 177 5 %RANDOM
Rwork0.191 ---
obs-4072 --
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms802 0 0 58 860
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_mcbond_it3.021.5
X-RAY DIFFRACTIONr_mcangle_it4.932
X-RAY DIFFRACTIONr_scbond_it42
X-RAY DIFFRACTIONr_scangle_it5.542.5

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