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

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Basic information

Entry
Database: PDB / ID: 6yiw
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
1H-isoindol-3-amine / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 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 2.0Mar 3, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.occupancy / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_seq_num / _struct_site_gen.auth_seq_id
Revision 2.1Jan 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 2.2Oct 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

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,09710
Polymers23,3241
Non-polymers7739
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-32 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.258, 58.156, 66.863
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 280 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-F05 / 1H-isoindol-3-amine


Mass: 132.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 39.91 %
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: 14.1 / 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: 0.97→50 Å / Num. obs: 125036 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 7.55 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.02
Reflection shellResolution: 0.97→1.03 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.23 / Num. unique obs: 19736 / CC1/2: 0.816 / % possible all: 98.1

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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: 0.97→42.13 Å / SU ML: 0.0627 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.9381
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1421 6251 5 %
Rwork0.1302 118765 -
obs0.1308 125016 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.25 Å2
Refinement stepCycle: LAST / Resolution: 0.97→42.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 42 271 1933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561888
X-RAY DIFFRACTIONf_angle_d0.97512593
X-RAY DIFFRACTIONf_chiral_restr0.0852282
X-RAY DIFFRACTIONf_plane_restr0.0073350
X-RAY DIFFRACTIONf_dihedral_angle_d14.381695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.980.23271920.23223645X-RAY DIFFRACTION92.37
0.98-0.990.23472040.22073883X-RAY DIFFRACTION99.46
0.99-10.22162070.20443945X-RAY DIFFRACTION99.69
1-1.020.1942050.19763893X-RAY DIFFRACTION99.44
1.02-1.030.19682070.17893940X-RAY DIFFRACTION99.71
1.03-1.040.1572070.16863931X-RAY DIFFRACTION99.57
1.04-1.060.17952070.1583928X-RAY DIFFRACTION99.59
1.06-1.070.17622050.14973898X-RAY DIFFRACTION99.42
1.07-1.090.14242080.12873943X-RAY DIFFRACTION99.81
1.09-1.110.11232070.11563938X-RAY DIFFRACTION99.76
1.11-1.130.12052080.10763946X-RAY DIFFRACTION99.86
1.13-1.150.13392080.10873944X-RAY DIFFRACTION99.81
1.15-1.170.12612060.10453919X-RAY DIFFRACTION99.59
1.17-1.20.122100.10473983X-RAY DIFFRACTION99.81
1.2-1.220.11392060.10683930X-RAY DIFFRACTION99.88
1.22-1.250.12132080.10423952X-RAY DIFFRACTION99.95
1.25-1.280.11162090.11013962X-RAY DIFFRACTION99.86
1.28-1.320.13082080.11443964X-RAY DIFFRACTION99.78
1.32-1.350.14732090.11343966X-RAY DIFFRACTION99.88
1.35-1.40.12832090.11423957X-RAY DIFFRACTION99.9
1.4-1.450.11392090.11193980X-RAY DIFFRACTION99.76
1.45-1.510.13072100.11253986X-RAY DIFFRACTION99.81
1.51-1.570.112090.11313971X-RAY DIFFRACTION99.93
1.57-1.660.1422100.11443991X-RAY DIFFRACTION99.83
1.66-1.760.12262110.11734010X-RAY DIFFRACTION99.74
1.76-1.90.13822090.12243977X-RAY DIFFRACTION99.57
1.9-2.090.13712120.11764033X-RAY DIFFRACTION99.6
2.09-2.390.11052130.1224032X-RAY DIFFRACTION99.93
2.39-3.010.14172150.13814083X-RAY DIFFRACTION99.7
3.01-42.130.18492230.15834235X-RAY DIFFRACTION99.27

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