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- PDB-1wbc: CRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES OF PSOPHOCARPIN B1,... -

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Basic information

Entry
Database: PDB / ID: 1wbc
TitleCRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES OF PSOPHOCARPIN B1, A CHYMOTRYPSIN INHIBITOR FROM WINGED BEAN SEEDS
ComponentsCHYMOTRYPSIN INHIBITOR (WCI)
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: 2.95 Å
AuthorsDattagupta, J.K. / Podder, A. / Chakrabarti, C. / Sen, U. / Dutta, S.K. / Singh, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of a Kunitz-type chymotrypsin from winged bean seeds at 2.95 A resolution.
Authors: Dattagupta, J.K. / Podder, A. / Chakrabarti, C. / Sen, U. / Dutta, S.K. / Singh, M.
History
DepositionNov 30, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Remark 700SHEET WCI HAS BEEN FOUND TO BE SPHERICAL AND CONSISTS OF 12 ANTIPARALLEL BETA-STRANDS WITH ...SHEET WCI HAS BEEN FOUND TO BE SPHERICAL AND CONSISTS OF 12 ANTIPARALLEL BETA-STRANDS WITH CONNECTING LOOPS ARRANGED IN A CHARACTERISTIC FOLDING - A SIX-STRANDED BETA-BARREL AND A SIX-STRANDED LID (COMPRISING OF THREE PAIRS OF ANTIPARALLEL B-STRANDS) ON ONE HOLLOW END OF THE BARREL. 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHYMOTRYPSIN INHIBITOR (WCI)


Theoretical massNumber of molelcules
Total (without water)20,2671
Polymers20,2671
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.400, 61.400, 210.900
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 / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.67 mg/mlprotein1drop
28.3 %ammonium sulfate1drop
30.1 MTris-HCl1drop
425 %ammonium sulfate1reservoir
50.1 MTris-HCl1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.95 Å / Num. obs: 3913 / % possible obs: 85 % / Num. measured all: 9549 / Rmerge(I) obs: 0.046

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.95→8 Å
Details: THE ELECTRON DENSITY IS CONTINUOUS FOR ALL THE MAIN CHAIN ATOMS EXCEPT FOR RESIDUES 179 AND 180 NEAR THE C-TERMINUS. HOWEVER THE FITTING OF THE MODEL TO THE ELECTRON DENSITY MAP IN THE ...Details: THE ELECTRON DENSITY IS CONTINUOUS FOR ALL THE MAIN CHAIN ATOMS EXCEPT FOR RESIDUES 179 AND 180 NEAR THE C-TERMINUS. HOWEVER THE FITTING OF THE MODEL TO THE ELECTRON DENSITY MAP IN THE RESIDUE RANGES 107 - 113, 136 - 143, AND 152 - 157 IS SOMEWHAT POOR.
RfactorNum. reflection
Rwork0.191 -
obs0.191 3703
Refinement stepCycle: LAST / Resolution: 2.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 0 56 1471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg28.1
X-RAY DIFFRACTIONx_improper_angle_deg1.9

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