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- PDB-3rdy: Crystal Structure of buckwheat trypsin inhibitor rBTI at 1.84 ang... -

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Basic information

Entry
Database: PDB / ID: 3rdy
TitleCrystal Structure of buckwheat trypsin inhibitor rBTI at 1.84 angstrom resolution
ComponentsBWI-1=PROTEASE inhibitor/trypsin inhibitor
KeywordsHYDROLASE INHIBITOR / serine protease inhibitor / potato inhibitor I / trypsin inhibitor / trypsin
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / response to wounding
Similarity search - Function
Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proteinase inhibitor
Similarity search - Component
Biological speciesFagopyrum esculentum (common buckwheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsWang, L.F. / Li, M. / Chang, W.R.
CitationJournal: Plos One / Year: 2011
Title: Conformational Changes of rBTI from Buckwheat upon Binding to Trypsin: Implications for the Role of the P(8)' Residue in the Potato Inhibitor I Family
Authors: Wang, L.F. / Zhao, F. / Li, M. / Zhang, H. / Gao, Y. / Cao, P. / Pan, X. / Wang, Z. / Chang, W.R.
History
DepositionApr 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BWI-1=PROTEASE inhibitor/trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)9,0191
Polymers9,0191
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.654, 62.654, 45.906
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 BWI-1=PROTEASE inhibitor/trypsin inhibitor / Proteinase inhibitor


Mass: 9019.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fagopyrum esculentum (common buckwheat)
Gene: BWI-1, Edn1 / Plasmid: QIA express pQE-31 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9S9F3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 24% (w/v) PEG MME 2000, 220mM ammonium sulfate, 100mM sodium acetate (pH 4.4), 100mM sodium iodide, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 3, 2009
RadiationMonochromator: Si(111) double flat-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→15 Å / Num. all: 8360 / Num. obs: 8344 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 24.1 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 46.4
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 23.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RDZ

3rdz


Resolution: 1.84→14.464 Å / FOM work R set: 0.856 / SU ML: 0.16 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 20.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 397 4.76 %random
Rwork0.1905 ---
all0.1935 8360 --
obs0.1916 8344 55.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.987 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.8042 Å2-0 Å2-0 Å2
2---5.8042 Å2-0 Å2
3----4.376 Å2
Refinement stepCycle: LAST / Resolution: 1.84→14.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms494 0 0 92 586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012503
X-RAY DIFFRACTIONf_angle_d1.39685
X-RAY DIFFRACTIONf_dihedral_angle_d14.765181
X-RAY DIFFRACTIONf_chiral_restr0.09981
X-RAY DIFFRACTIONf_plane_restr0.00690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8391-2.10460.2631320.19552581X-RAY DIFFRACTION54
2.1046-2.64890.22231450.17932596X-RAY DIFFRACTION54
2.6489-14.4640.19831200.19292769X-RAY DIFFRACTION57

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