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- PDB-4gux: Crystal structure of trypsin:MCoTi-II complex -

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Basic information

Entry
Database: PDB / ID: 4gux
TitleCrystal structure of trypsin:MCoTi-II complex
Components
  • Cationic trypsin
  • Trypsin inhibitor 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cyclotide / cyclic peptide / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of serine-type endopeptidase activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / defense response / endopeptidase activity / serine-type endopeptidase activity / proteolysis ...negative regulation of serine-type endopeptidase activity / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / defense response / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Plant trypsin inhibitors / Proteinase inhibitor I7, squash / Squash family serine protease inhibitor / Squash family of serine protease inhibitors signature. / Proteinase/amylase inhibitor domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. ...Plant trypsin inhibitors / Proteinase inhibitor I7, squash / Squash family serine protease inhibitor / Squash family of serine protease inhibitors signature. / Proteinase/amylase inhibitor domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CYCLIC KNOTTIN TRYPSIN INHIBITOR II / ACETATE ION / Serine protease 1 / Trypsin inhibitor 2
Similarity search - Component
Biological speciesBos taurus (cattle)
Momordica cochinchinensis (spiny bitter cucumber)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsKing, G.J. / Daly, N.L. / Thorstholm, L. / Greenwood, K.P. / Rosengren, K.J. / Heras, B. / Craik, D.J. / Martin, J.L.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural insights into the role of the cyclic backbone in a squash trypsin inhibitor
Authors: Daly, N.L. / Thorstholm, L. / Greenwood, K.P. / King, G.J. / Rosengren, K.J. / Heras, B. / Martin, J.L. / Craik, D.J.
History
DepositionAug 30, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Cationic trypsin
B: Cationic trypsin
C: Cationic trypsin
D: Trypsin inhibitor 2
E: Trypsin inhibitor 2
F: Trypsin inhibitor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,10611
Polymers87,8686
Non-polymers2385
Water22,0681225
1
A: Cationic trypsin
D: Trypsin inhibitor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3884
Polymers29,2892
Non-polymers992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-22 kcal/mol
Surface area10090 Å2
MethodPISA
2
B: Cationic trypsin
E: Trypsin inhibitor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3884
Polymers29,2892
Non-polymers992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-23 kcal/mol
Surface area10110 Å2
MethodPISA
3
C: Cationic trypsin
F: Trypsin inhibitor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3293
Polymers29,2892
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-22 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.139, 71.852, 108.460
Angle α, β, γ (deg.)90.00, 119.76, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

21B-579-

HOH

31C-469-

HOH

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Components

#1: Protein Cationic trypsin / Beta-trypsin / Alpha-trypsin chain 1 / Alpha-trypsin chain 2


Mass: 25806.197 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein/peptide Trypsin inhibitor 2 / MCoTI-II / Trypsin inhibitor II


Type: Cyclic peptide / Class: Antimicrobial, Antitumor / Mass: 3483.040 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Momordica cochinchinensis (spiny bitter cucumber)
References: UniProt: P82409, CYCLIC KNOTTIN TRYPSIN INHIBITOR II
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1225 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG3350, 0.24M ammonium acetate, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953645 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 1, 2009
RadiationMonochromator: monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953645 Å / Relative weight: 1
ReflectionResolution: 1.8→31.69 Å / Num. all: 82578 / Num. obs: 82545 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.449 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UUY

2uuy


Resolution: 1.803→31.69 Å / SU ML: 0.21 / Cross valid method: Rfree / σ(F): 1.34 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1941 4122 4.99 %5% random
Rwork0.1573 ---
obs0.1615 82545 98.46 %-
all-82578 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.038 Å2 / ksol: 0.355 e/Å3
Refinement stepCycle: LAST / Resolution: 1.803→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5591 0 11 1225 6827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065835
X-RAY DIFFRACTIONf_angle_d1.0227895
X-RAY DIFFRACTIONf_dihedral_angle_d11.4462115
X-RAY DIFFRACTIONf_chiral_restr0.073881
X-RAY DIFFRACTIONf_plane_restr0.0041026
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.803-1.86740.24613850.2196759395
1.8674-1.94220.26044160.2168775798
1.9422-2.03050.21554110.1603776598
2.0305-2.13760.21584210.1718780298
2.1376-2.27140.21163980.1712779698
2.2714-2.44680.18524010.1508786499
2.4468-2.69290.16784210.1464785099
2.6929-3.08230.19664010.1562795699
3.0823-3.88220.16484440.1457938100
3.8822-31.69840.15174240.14388102100

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