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- PDB-1eyl: STRUCTURE OF A RECOMBINANT WINGED BEAN CHYMOTRYPSIN INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1eyl
TitleSTRUCTURE OF A RECOMBINANT WINGED BEAN CHYMOTRYPSIN INHIBITOR
ComponentsCHYMOTRYPSIN INHIBITOR
KeywordsHYDROLASE INHIBITOR / BETA TREFOIL
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 / SYNCHROTRON / Resolution: 1.9 Å
AuthorsDattagupta, J.K. / Chakrabarti, C. / Ravichandran, S. / Ghosh, S.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Cryocrystallography of a Kunitz-type serine protease inhibitor: the 90 K structure of winged bean chymotrypsin inhibitor (WCI) at 2.13 A resolution
Authors: Ravichandran, S. / Sen, U. / Chakrabarti, C. / Dattagupta, J.K.
#2: 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.
#3: Journal: Protein Expr.Purif. / Year: 1997
Title: cDNA Cloning, Expression, and Rapid Purification of a Kunitz-Type Winged Bean Chymotrypsin Inhibitor
Authors: Ghosh, S. / Singh, M.
History
DepositionMay 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_ref_seq_dif ...database_2 / struct_ref_seq_dif / struct_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHYMOTRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1556
Polymers20,6741
Non-polymers4805
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: CHYMOTRYPSIN INHIBITOR
hetero molecules

A: CHYMOTRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,30912
Polymers41,3492
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area3080 Å2
ΔGint-167 kcal/mol
Surface area18470 Å2
MethodPISA
3
A: CHYMOTRYPSIN INHIBITOR
hetero molecules

A: CHYMOTRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,30912
Polymers41,3492
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_435x-y-1,-y-2,-z1
Buried area2960 Å2
ΔGint-155 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.760, 60.760, 208.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-900-

SO4

21A-501-

HOH

DetailsThe biological assembly is a monomer constructed from chain A

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Components

#1: Protein CHYMOTRYPSIN INHIBITOR / RWCI-3


Mass: 20674.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psophocarpus tetragonolobus (winged bean)
Organ: SEED / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / References: UniProt: P10822
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.4
Details: ammonium sulfate, sodium acetate, pH 5.4, VAPOR DIFFUSION, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 17, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 124633 / Num. obs: 18807 / % possible obs: 99.7 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 6.6 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 6.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.202 / Num. unique all: 2649 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
REFMACrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 1.9→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood (MLK) target function.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1876 -RANDOM
Rwork0.195 ---
all0.233 18725 --
obs0.233 18701 99.4 %-
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1400 0 25 190 1615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_deg0.023

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