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- PDB-2qyi: Crystal structure of a binary complex between an engineered tryps... -

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Basic information

Entry
Database: PDB / ID: 2qyi
TitleCrystal structure of a binary complex between an engineered trypsin inhibitor and Bovine trypsin
Components
  • Cationic trypsin
  • Chymotrypsin inhibitor 3
KeywordsHydrolase/Hydrolase inhibitor / P1 mutant / trypsin inhibitor / bovine trypsin / complex / Calcium / Digestion / Hydrolase / Metal-binding / Protease / Secreted / Serine protease / Zymogen / Protease inhibitor / Serine protease inhibitor / Hydrolase-Hydrolase inhibitor COMPLEX
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site ...Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Serine protease 1 / Chymotrypsin inhibitor 3
Similarity search - Component
Biological speciesBos taurus (cattle)
Psophocarpus tetragonolobus (winged bean)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsKhamrui, S. / Dasgupta, J. / Dattagupta, J.K. / Sen, U.
Citation
Journal: To be Published
Title: Crystal structure of a binary complex between an engineered trypsin inhibitor and Bovine trypsin
Authors: Sen, U.
#1: Journal: Biochim.Biophys.Acta / Year: 2005
Title: Single mutation at P1 of a chymotrypsin inhibitor changes it to a trypsin inhibitor: X-ray structural (2.15 A) and biochemical basis
Authors: Khamrui, S. / Dasgupta, J. / Dattagupta, J.K. / Sen, U.
History
DepositionAug 15, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
B: Chymotrypsin inhibitor 3
C: Cationic trypsin
D: Chymotrypsin inhibitor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4097
Polymers87,2704
Non-polymers1393
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
Unit cell
Length a, b, c (Å)143.694, 77.437, 72.907
Angle α, β, γ (deg.)90.000, 103.000, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00760
#2: Protein Chymotrypsin inhibitor 3 / WCI-3


Mass: 20310.885 Da / Num. of mol.: 2 / Mutation: L68R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psophocarpus tetragonolobus (winged bean)
Production host: Escherichia coli (E. coli) / References: UniProt: P10822
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 30% Jefamine, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 23234 / Redundancy: 2.91 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3data extraction
RefinementResolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.268 1133 4.7 %
Rwork0.208 --
obs-23193 96.3 %
Solvent computationBsol: 33.746 Å2
Displacement parametersBiso mean: 30.282 Å2
Baniso -1Baniso -2Baniso -3
1--10.677 Å20 Å22.757 Å2
2--3.184 Å20 Å2
3---7.493 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6000 0 3 312 6315
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.544
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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