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- PDB-1fn0: STRUCTURE OF A MUTANT WINGED BEAN CHYMOTRYPSIN INHIBITOR PROTEIN,... -

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Basic information

Entry
Database: PDB / ID: 1fn0
TitleSTRUCTURE OF A MUTANT WINGED BEAN CHYMOTRYPSIN INHIBITOR PROTEIN, N14D.
ComponentsCHYMOTRYPSIN INHIBITOR 3
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: 2 Å
AuthorsDattagupta, J.K. / Chakrabarti, C. / Ravichandran, S. / Dasgupta, J. / 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: Crystallography of a Kunitz-type Serine Protease Inhibitor: The 90K Structure of Winged bean Chymotrypsin Inhibitor (WCI) at 2.13A resolution.
Authors: Ravichandran, S. / Sen, U. / Chakrabarti, C. / Dattagupta, J.K.
#2: Journal: Proteins / Year: 1999
Title: Refined crystal structure (2.3A) 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 Kunitz-type Winged bean Chymotrypsin Inhibitor
Authors: Dattagupta, J.K. / Chakrabarti, C. / Ravichandran, S. / Dasgupta, J. / Ghosh, S.
History
DepositionAug 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 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
Revision 1.4Oct 30, 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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0605
Polymers20,6751
Non-polymers3844
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CHYMOTRYPSIN INHIBITOR 3
hetero molecules

A: CHYMOTRYPSIN INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,11910
Polymers41,3512
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area2680 Å2
ΔGint-141 kcal/mol
Surface area18500 Å2
MethodPISA
3
A: CHYMOTRYPSIN INHIBITOR 3
hetero molecules

A: CHYMOTRYPSIN INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,11910
Polymers41,3512
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_435x-y-1,-y-2,-z1
Buried area2310 Å2
ΔGint-99 kcal/mol
Surface area18490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.240, 61.240, 210.860
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

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Components

#1: Protein CHYMOTRYPSIN INHIBITOR 3 / WCI-3


Mass: 20675.316 Da / Num. of mol.: 1 / Mutation: N14D
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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: Ammonium sulfate, Sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Details: Dattagupta, J.K., (1999) Proteins: Struct., Funct., Genet., 35, 321.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.6 mg/mlprotein1drop
271.4 mMTris-HCl1drop
3286 mM1dropNaCl
41.4 %ammonium sulfate1drop
52.9 mMsodium acetate1drop
625 %ammonium sulfate1reservoir
760 mMsodium acetate1reservoir

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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: Aug 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→18 Å / Num. all: 33037 / Num. obs: 14503 / % possible obs: 75.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 3.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.423 / % possible all: 75.7
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 33037
Reflection shell
*PLUS
% possible obs: 68.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4(SCALA)data scaling
RefinementResolution: 2→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1249 -RANDOM
Rwork0.209 ---
all0.217 33037 --
obs0.217 11351 76.1 %-
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1384 0 20 169 1573
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.027
X-RAY DIFFRACTIONp_angle_d2.1
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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