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- PDB-4wbc: 2.13 A STRUCTURE OF A KUNITZ-TYPE WINGED BEAN CHYMOTRYPSIN INHIBI... -

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Basic information

Entry
Database: PDB / ID: 4wbc
Title2.13 A STRUCTURE OF A KUNITZ-TYPE WINGED BEAN CHYMOTRYPSIN INHIBITOR PROTEIN
ComponentsPROTEIN (CHYMOTRYPSIN 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 / OTHER / Resolution: 2.138 Å
AuthorsRavichandran, S. / Sen, U. / Chakrabarti, C. / Dattagupta, J.K.
Citation
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.
#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: 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.
#3: 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
DepositionMar 4, 1999Deposition site: BNL / Processing site: RCSB
SupersessionMar 12, 1999ID: 3WBC
Revision 1.0Mar 12, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CHYMOTRYPSIN INHIBITOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7476
Polymers20,2671
Non-polymers4805
Water3,171176
1


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

A: PROTEIN (CHYMOTRYPSIN INHIBITOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,49412
Polymers40,5342
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area3110 Å2
ΔGint-176 kcal/mol
Surface area18490 Å2
MethodPISA
3
A: PROTEIN (CHYMOTRYPSIN INHIBITOR)
hetero molecules

A: PROTEIN (CHYMOTRYPSIN INHIBITOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,49412
Polymers40,5342
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_435x-y-1,-y-2,-z1
Buried area3080 Å2
ΔGint-163 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.840, 60.840, 207.910
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-194-

SO4

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Components

#1: Protein 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: 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.: 176 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE PRESENCE OF SULPHATE IONS IN THE STRUCTURE IS DUE TO THE PRESENCE OF AMMONIUM SULPHATE SALT ...THE PRESENCE OF SULPHATE IONS IN THE STRUCTURE IS DUE TO THE PRESENCE OF AMMONIUM SULPHATE SALT USED IN THE CRYSTALLIZATION BUFFER.
Sequence detailsREFERENCE: THE SEQUENCE OF WCI WAS TAKEN FROM SHIBATA, J. BIOCHEM. VOL. 134, 537-543, 1988.

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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: 2.69 Å3/Da / Density % sol: 54 %
Description: THE CRYSTALS WERE MOUNTED IN A HAIR (HUMAN) LOOP AND FLASH FROZEN IN A STREAM OF LIQUID NITROGEN GAS STREAM AT 90 K FOR DATA COLLECTION.
Crystal growpH: 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 DEG. C. ...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 DEG. C. CRYSTALS WERE THEN TRANSFERED TO 25% GLYCEROL (CRYOPROTECTANT) IN 25% AMM. SULPHATE, 10MM NA ACETATE BUFFER AT PH 5.4, BEFORE FLASH COOLING.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
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
710 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: DOUBLE FOCUSSING MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.138→15 Å / Num. obs: 12963 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13
Reflection shellResolution: 2.13→2.18 Å / Rmerge(I) obs: 0.236 / % possible all: 64.5
Reflection
*PLUS
Num. measured all: 63933

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: OTHER / Resolution: 2.138→9 Å / SU B: 3.02 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.22
Details: PDB ENTRY 2WBC IS THE STARTING MODEL FOR REFINEMENT. INITIAL REFINEMENTS WERE DONE USING XPLOR 3.851
RfactorNum. reflection% reflectionSelection details
Rfree0.257 -10 %RANDOM
Rwork0.199 ---
obs-11100 93.6 %-
Displacement parametersBiso mean: 32.7 Å2
Refinement stepCycle: LAST / Resolution: 2.138→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 25 176 1602
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0270.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.043
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.932
X-RAY DIFFRACTIONp_mcangle_it5.333
X-RAY DIFFRACTIONp_scbond_it4.472
X-RAY DIFFRACTIONp_scangle_it6.283
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.1230.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.2580.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1670.3
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor18.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor37.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 9 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_mcbond_it3.932
X-RAY DIFFRACTIONp_scbond_it4.472
X-RAY DIFFRACTIONp_mcangle_it5.333
X-RAY DIFFRACTIONp_scangle_it6.283

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