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- PDB-6yiv: Trypsin inhibitor in complex with bovine trypsin -

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Basic information

Entry
Database: PDB / ID: 6yiv
TitleTrypsin inhibitor in complex with bovine trypsin
ComponentsCationic trypsin
KeywordsHYDROLASE / Fragment / protease / Serine protease
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / 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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / 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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
[azanyl(piperidin-1-yl)methylidene]azanium / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsBadran, M.J. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Trypsin inhibitor in complex with bovine trypsin
Authors: Badran, M.J. / Heine, A. / Klebe, G.
History
DepositionApr 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,22711
Polymers23,3241
Non-polymers90310
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-35 kcal/mol
Surface area9170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.264, 58.164, 67.093
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-D86 / [azanyl(piperidin-1-yl)methylidene]azanium


Mass: 128.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: ammonium sulfat, PEG 8000, ethylene glycol, HEPES / PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 29, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.95→50 Å / Num. obs: 130966 / % possible obs: 97.7 % / Redundancy: 4.63 % / Biso Wilson estimate: 6.75 Å2 / CC1/2: 1 / Net I/σ(I): 29.44
Reflection shellResolution: 0.95→1.01 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.56 / Num. unique obs: 19891 / CC1/2: 0.94 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mnk

5mnk


Resolution: 0.95→29.06 Å / SU ML: 0.0501 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 10.5915
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1345 6541 5 %
Rwork0.1248 124291 -
obs0.1252 130832 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.05 Å2
Refinement stepCycle: LAST / Resolution: 0.95→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1621 0 49 292 1962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561864
X-RAY DIFFRACTIONf_angle_d0.97712550
X-RAY DIFFRACTIONf_chiral_restr0.0874278
X-RAY DIFFRACTIONf_plane_restr0.0079331
X-RAY DIFFRACTIONf_dihedral_angle_d13.6737683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.960.18531870.17033532X-RAY DIFFRACTION83.89
0.96-0.970.17632020.15773836X-RAY DIFFRACTION90.95
0.97-0.980.15642050.15223942X-RAY DIFFRACTION94.66
0.98-10.172140.14454049X-RAY DIFFRACTION96.78
1-1.010.15292170.13344115X-RAY DIFFRACTION97.13
1.01-1.020.14632140.12784070X-RAY DIFFRACTION96.92
1.02-1.040.13822150.11974098X-RAY DIFFRACTION97.54
1.04-1.050.13682150.10894089X-RAY DIFFRACTION97.35
1.05-1.070.1142150.10764092X-RAY DIFFRACTION97.2
1.07-1.090.10762170.09944115X-RAY DIFFRACTION97.57
1.09-1.110.1042190.09474147X-RAY DIFFRACTION97.94
1.11-1.130.11432140.09114068X-RAY DIFFRACTION98.01
1.13-1.150.10572170.09424150X-RAY DIFFRACTION98.13
1.15-1.170.10982190.09664138X-RAY DIFFRACTION98.11
1.17-1.20.11412190.09764166X-RAY DIFFRACTION98.52
1.2-1.220.13152180.10494157X-RAY DIFFRACTION98.62
1.22-1.260.11882190.10094161X-RAY DIFFRACTION98.38
1.26-1.290.12572210.10694194X-RAY DIFFRACTION98.55
1.29-1.330.10612200.10944172X-RAY DIFFRACTION98.61
1.33-1.370.1072210.1144211X-RAY DIFFRACTION99.44
1.37-1.420.12632210.10764199X-RAY DIFFRACTION99.3
1.42-1.480.12572210.10844195X-RAY DIFFRACTION99.01
1.48-1.540.11452230.11094230X-RAY DIFFRACTION99.6
1.54-1.620.12142230.11534251X-RAY DIFFRACTION99.55
1.62-1.730.13992240.11794251X-RAY DIFFRACTION99.73
1.73-1.860.1412250.12314267X-RAY DIFFRACTION99.73
1.86-2.050.12962230.12434234X-RAY DIFFRACTION98.78
2.05-2.340.12412270.12264322X-RAY DIFFRACTION99.61
2.34-2.950.12712280.14534334X-RAY DIFFRACTION99.5
2.95-29.060.17992380.16214506X-RAY DIFFRACTION99.35

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