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

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Basic information

Entry
Database: PDB / ID: 6yzc
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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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
DepositionMay 6, 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 1.2Nov 6, 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)23,5844
Polymers23,3241
Non-polymers2593
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-4 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.614, 54.614, 107.478
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-570-

HOH

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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 (domestic cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-AMH / TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID


Mass: 157.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.94 Å3/Da / Density % sol: 36.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: ammonium sulfate, PEG 8000, ethylene glycol, HEPES

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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: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 26, 2018
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: 1.42→50 Å / Num. obs: 35782 / % possible obs: 99.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 17.03 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.66
Reflection shellResolution: 1.42→1.51 Å / Mean I/σ(I) obs: 3.35 / Num. unique obs: 5703 / CC1/2: 0.91

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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: 1.42→43.29 Å / SU ML: 0.1368 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.7334
RfactorNum. reflection% reflection
Rfree0.1792 1790 5 %
Rwork0.1426 --
obs0.1444 35780 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.34 Å2
Refinement stepCycle: LAST / Resolution: 1.42→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 0 16 176 1800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671712
X-RAY DIFFRACTIONf_angle_d0.91592333
X-RAY DIFFRACTIONf_chiral_restr0.0838266
X-RAY DIFFRACTIONf_plane_restr0.0063301
X-RAY DIFFRACTIONf_dihedral_angle_d12.3766624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.460.25881350.17612556X-RAY DIFFRACTION99.81
1.46-1.50.20861360.14942583X-RAY DIFFRACTION99.96
1.5-1.550.19421350.13862568X-RAY DIFFRACTION99.63
1.55-1.60.21581370.13952608X-RAY DIFFRACTION100
1.6-1.670.23321340.12972545X-RAY DIFFRACTION100
1.67-1.750.19291380.12482608X-RAY DIFFRACTION99.96
1.75-1.840.18241360.12142595X-RAY DIFFRACTION100
1.84-1.950.16941360.12012588X-RAY DIFFRACTION99.53
1.95-2.10.15181390.11952625X-RAY DIFFRACTION100
2.1-2.310.1541370.12752615X-RAY DIFFRACTION100
2.31-2.650.17571390.13662634X-RAY DIFFRACTION99.86
2.65-3.340.19991400.14712669X-RAY DIFFRACTION99.79
3.34-43.290.1691480.16472796X-RAY DIFFRACTION99.73

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