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- PDB-3ci7: Crystal structure of a simplified BPTI containing 20 alanines -

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Basic information

Entry
Database: PDB / ID: 3ci7
TitleCrystal structure of a simplified BPTI containing 20 alanines
Componentsbovine pancreatic trypsin inhibitor
KeywordsHYDROLASE INHIBITOR / sequence simplification / bovine pancreatic trypsin inhibitor
Function / homologyPancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Few Secondary Structures / Irregular
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.4 Å
AuthorsIslam, M.M. / Sohya, S. / Noguchi, K. / Yohda, M. / Kuroda, Y.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines
Authors: Islam, M.M. / Sohya, S. / Noguchi, K. / Yohda, M. / Kuroda, Y.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 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: bovine pancreatic trypsin inhibitor
B: bovine pancreatic trypsin inhibitor
C: bovine pancreatic trypsin inhibitor
D: bovine pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2198
Polymers23,8354
Non-polymers3844
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-66.6 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.508, 57.222, 71.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
bovine pancreatic trypsin inhibitor / BPTI


Mass: 5958.770 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Peptide synthesis
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.13 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: Tris-HCl, pH8.7, Lithium sulfate, PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→44.76 Å / Num. all: 40883 / Num. obs: 38836
Reflection shellHighest resolution: 1.4 Å / Num. unique all: 40883

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB entry 5PTI

5pti


Resolution: 1.4→44.76 Å / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 2047 -RANDOM
obs0.1513 38836 99.7 %-
all-40883 --
Refine analyzeNum. disordered residues: 2
Refinement stepCycle: LAST / Resolution: 1.4→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 20 277 1948

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