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

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Basic information

Entry
Database: PDB / ID: 6yza
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 / digestion / serine protease inhibitor complex / 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 domain profile. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
THIOPHENE-3-CARBOXIMIDAMIDE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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

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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)23,7116
Polymers23,3241
Non-polymers3865
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-24 kcal/mol
Surface area8820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.739, 54.739, 107.104
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

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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, 180 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TP5 / THIOPHENE-3-CARBOXIMIDAMIDE


Mass: 126.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.84 %
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: 1.3→50 Å / Num. obs: 46289 / % possible obs: 99.5 % / Redundancy: 20 % / Biso Wilson estimate: 16.31 Å2 / CC1/2: 0.99 / Net I/σ(I): 21.04
Reflection shellResolution: 1.3→1.38 Å / Mean I/σ(I) obs: 5.68 / Num. unique obs: 7308 / CC1/2: 0.96

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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: 1.3→35.7 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.6039
RfactorNum. reflection% reflection
Rfree0.1734 2314 5 %
Rwork0.1507 --
obs0.1518 46286 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.88 Å2
Refinement stepCycle: LAST / Resolution: 1.3→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 0 22 175 1797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651702
X-RAY DIFFRACTIONf_angle_d0.92252320
X-RAY DIFFRACTIONf_chiral_restr0.0832262
X-RAY DIFFRACTIONf_plane_restr0.007306
X-RAY DIFFRACTIONf_dihedral_angle_d12.4775613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.19891320.1512498X-RAY DIFFRACTION98.02
1.33-1.350.19671340.14582545X-RAY DIFFRACTION98.67
1.35-1.390.22161320.14512515X-RAY DIFFRACTION98.92
1.39-1.420.18541340.13712543X-RAY DIFFRACTION98.96
1.42-1.460.16771330.13642531X-RAY DIFFRACTION99.11
1.46-1.50.16951350.12672567X-RAY DIFFRACTION99.23
1.5-1.550.18551340.12512541X-RAY DIFFRACTION99.26
1.55-1.610.15641360.12482596X-RAY DIFFRACTION99.49
1.61-1.670.15291350.12692553X-RAY DIFFRACTION99.63
1.67-1.750.17341350.12762573X-RAY DIFFRACTION99.67
1.75-1.840.14821360.13222578X-RAY DIFFRACTION99.85
1.84-1.950.17081380.13232619X-RAY DIFFRACTION99.96
1.95-2.10.15941370.13062606X-RAY DIFFRACTION100
2.1-2.320.14861370.14292605X-RAY DIFFRACTION100
2.32-2.650.18871390.15012632X-RAY DIFFRACTION100
2.65-3.340.1771400.16322669X-RAY DIFFRACTION100
3.34-35.70.1811470.17342801X-RAY DIFFRACTION99.93

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