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- PDB-3qyd: Crystal structure of a recombinant chimeric trypsin inhibitor -

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Basic information

Entry
Database: PDB / ID: 3qyd
TitleCrystal structure of a recombinant chimeric trypsin inhibitor
ComponentsChymotrypsin inhibitor 3
KeywordsHYDROLASE INHIBITOR / recombinant protein / mutant / trypsin inhibitor / chimeric protein beta barrel fold
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity
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 / Mainly Beta
Similarity search - Domain/homology
Chymotrypsin inhibitor 3
Similarity search - Component
Biological speciesPsophocarpus tetragonolobus (winged bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsSen, U. / Majumder, S. / Khamrui, S. / Dasgupta, J.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: Role of remote scaffolding residues in the inhibitory loop pre-organization, flexibility, rigidification and enzyme inhibition of serine protease inhibitors
Authors: Majumder, S. / Khamrui, S. / Dasgupta, J. / Dattagupta, J.K. / Sen, U.
History
DepositionMar 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 8, 2013Group: Database references
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: Chymotrypsin inhibitor 3
C: Chymotrypsin inhibitor 3
B: Chymotrypsin inhibitor 3


Theoretical massNumber of molelcules
Total (without water)60,6003
Polymers60,6003
Non-polymers00
Water2,594144
1
A: Chymotrypsin inhibitor 3


Theoretical massNumber of molelcules
Total (without water)20,2001
Polymers20,2001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Chymotrypsin inhibitor 3


Theoretical massNumber of molelcules
Total (without water)20,2001
Polymers20,2001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Chymotrypsin inhibitor 3


Theoretical massNumber of molelcules
Total (without water)20,2001
Polymers20,2001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.530, 39.250, 94.280
Angle α, β, γ (deg.)90.00, 118.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chymotrypsin inhibitor 3 / WCI-3


Mass: 20199.857 Da / Num. of mol.: 3 / Mutation: Q66R, F67L, L68R, L70A, A79R, L118Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psophocarpus tetragonolobus (winged bean)
Plasmid: PET28A+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10822
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 35% PEG, 0.1M Tris, 5% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Oct 8, 2010 / Details: mirors
RadiationMonochromator: Graphaite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.97→30 Å / Num. all: 12882 / Num. obs: 11790 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.35 % / Biso Wilson estimate: 65.094 Å2 / Rmerge(I) obs: 0.1181 / Net I/σ(I): 3.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.2refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3I2X

3i2x


Resolution: 2.97→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1170 -RANDOM
Rwork0.21 ---
all-12882 --
obs-11790 91.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.572 Å20 Å2-8.044 Å2
2---0.911 Å20 Å2
3----5.661 Å2
Refinement stepCycle: LAST / Resolution: 2.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4179 0 0 144 4323
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006876
X-RAY DIFFRACTIONc_angle_d1.67016

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