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- PDB-1xg6: The crystal structure of the P1 mutant (Leu to Arg)of a Winged be... -

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Basic information

Entry
Database: PDB / ID: 1xg6
TitleThe crystal structure of the P1 mutant (Leu to Arg)of a Winged bean chymotrypsin inhibitor(Kunitz)solved at 2.15A resolution
ComponentsChymotrypsin inhibitor 3
KeywordsHydrolase Inhibitor / trypsin inhibitor
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: 2.15 Å
AuthorsSen, U. / Dattagupta, J.K. / Dasgupta, J. / Khamrui, S.
Citation
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.
#1: Journal: Proteins / Year: 1999
Title: Refined crystal structure (2.3 A) of a double-headed winged bean alpha-chymotrypsin inhibitor and location of its second reactive site
Authors: Dattagupta, J.K. / Podder, A. / Chakrabarti, C. / Sen, U. / Mukhopadhyay, D. / Dutta, S.K. / Singh, M.
#2: Journal: Protein Eng. / Year: 2001
Title: The role of Asn14 in the stability and conformation of the reactive-site loop of winged bean chymotrypsin inhibitor: crystal structures of two point mutants Asn14-->Lys and Asn14-->Asp
Authors: Ravichandran, S. / Dasgupta, J. / Chakrabarti, C. / Ghosh, S. / Singh, M. / Dattagupta, J.K.
History
DepositionSep 16, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chymotrypsin inhibitor 3


Theoretical massNumber of molelcules
Total (without water)20,7241
Polymers20,7241
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.570, 99.570, 37.261
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Chymotrypsin inhibitor 3 / Winged bean chymotrypsin inhibitor / WCI-3


Mass: 20724.357 Da / Num. of mol.: 1 / Mutation: L68R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psophocarpus tetragonolobus (winged bean)
Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / References: UniProt: P10822
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.48 Å3/Da / Density % sol: 52.19 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 6, 2004 / Details: Osmic MaxFlux
RadiationMonochromator: Copper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→15 Å / Num. obs: 11202 / Biso Wilson estimate: 29.3 Å2

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Processing

Software
NameVersionClassification
CNS1refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYL

1eyl


Resolution: 2.15→14.93 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1249123.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 577 5.2 %RANDOM
Rwork0.199 ---
obs0.199 11202 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.5872 Å2 / ksol: 0.318978 e/Å3
Displacement parametersBiso mean: 45.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.79 Å23.75 Å20 Å2
2--5.79 Å20 Å2
3----11.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.15→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1399 0 0 190 1589
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it2.811.5
X-RAY DIFFRACTIONc_mcangle_it4.832
X-RAY DIFFRACTIONc_scbond_it3.522
X-RAY DIFFRACTIONc_scangle_it5.912.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 87 5.1 %
Rwork0.357 1625 -
obs--89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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