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- PDB-2wbc: REFINED CRYSTAL STRUCTURE (2.3 ANGSTROM) OF A WINGED BEAN CHYMOTR... -

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Basic information

Entry
Database: PDB / ID: 2wbc
TitleREFINED CRYSTAL STRUCTURE (2.3 ANGSTROM) OF A WINGED BEAN CHYMOTRYPSIN INHIBITOR AND LOCATION OF ITS SECOND REACTIVE SITE
ComponentsCHYMOTRYPSIN INHIBITOR
KeywordsSERINE PROTEASE 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 / Resolution: 2.3 Å
AuthorsDattagupta, J.K. / Podder, A. / Chakrabarti, C. / Sen, U. / Mukhopadhyay, D. / Dutta, S.K. / Singh, M.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization and Preliminary X-Ray Studies of Psophocarpin B1, a Chymotrypsin Inhibitor from Winged Bean Seeds
Authors: Dattagupta, J.K. / Chakrabarti, C. / Podder, A. / Dutta, S.K. / Singh, M.
History
DepositionNov 26, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHYMOTRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)20,2671
Polymers20,2671
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.800, 61.800, 212.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein CHYMOTRYPSIN INHIBITOR / WCI


Mass: 20266.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psophocarpus tetragonolobus (winged bean) / Tissue: SEED / References: UniProt: P10822
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.85 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP VAPOUR DIFFUSION FROM 25% AMM. SULPHATE IN TRIS-HCL, 10MM NA ACETATE,400 MM NACL AT PH 5.4 AGAINST 25% AMM. SULPHATE,60MM NA ACETATE AT 4 DEGREE ...Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP VAPOUR DIFFUSION FROM 25% AMM. SULPHATE IN TRIS-HCL, 10MM NA ACETATE,400 MM NACL AT PH 5.4 AGAINST 25% AMM. SULPHATE,60MM NA ACETATE AT 4 DEGREE CENTIGRADE., vapor diffusion - hanging drop, temperature 277K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
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: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→12 Å / Num. obs: 9897 / % possible obs: 80.1 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.095
Reflection
*PLUS
Num. measured all: 10551

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.3→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE ELECTRON DENSITY IS CONTINUOUS FOR ALL THE MAIN CHAIN ATOMS. HOWEVER THE FITTING OF THE MODEL TO THE ELECTRON DENSITY MAP IN THE RESIDUE RANGES 137 - 142, AND 176 - 183 IS SOMEWHAT POOR. ...Details: THE ELECTRON DENSITY IS CONTINUOUS FOR ALL THE MAIN CHAIN ATOMS. HOWEVER THE FITTING OF THE MODEL TO THE ELECTRON DENSITY MAP IN THE RESIDUE RANGES 137 - 142, AND 176 - 183 IS SOMEWHAT POOR. WCI HAS BEEN FOUND TO BE SPHERICAL AND CONSISTS OF 12 ANTIPARALLEL BETA-STRANDS WITH CONNECTING LOOPS ARRANGED IN A CHARACTERISTIC B-TREFOIL TYPE FOLDING. A PSEUDO THREE-FOLD AXIS EXISTS PARALLEL TO THE BARREL AXIS OF THE STRUCTURE. EACH OF THE THREE SUBDOMAINS COMPRISES FOUR B-STRANDS WITH CONNECTING LOOPS. FROM THIS HIGHER RESOLUTION MODEL THE LOCATION OF THE SECOND REACTIVE SITE OF THE INHIBITOR PROTEIN COULD BE IDENTIFIED MAINLY ON THE BASIS OF STRUCTURAL STUDIES.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 -10 %RANDOM
Rwork0.187 ---
obs0.187 9897 80.1 %-
Displacement parametersBiso mean: 30.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 0 109 1681
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.893
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.19
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.561
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.398
X-RAY DIFFRACTIONx_mcangle_it5.626
X-RAY DIFFRACTIONx_scbond_it4.768
X-RAY DIFFRACTIONx_scangle_it7.139
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.192
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.561

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