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- PDB-5mny: Neutron structure of cationic trypsin in complex with aniline -

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Basic information

Entry
Database: PDB / ID: 5mny
TitleNeutron structure of cationic trypsin in complex with aniline
ComponentsCationic trypsin
KeywordsHYDROLASE / hydrogen bonding / protonation / protein-ligand interaction
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
DEUTERATED WATER / phenylazanium / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsSchiebel, J. / Schrader, T.E. / Ostermann, A. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Charges Shift Protonation: Neutron Diffraction Reveals that Aniline and 2-Aminopyridine Become Protonated Upon Binding to Trypsin.
Authors: Schiebel, J. / Gaspari, R. / Sandner, A. / Ngo, K. / Gerber, H.D. / Cavalli, A. / Ostermann, A. / Heine, A. / Klebe, G.
History
DepositionDec 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 2.0Aug 23, 2017Group: Atomic model / Category: atom_site / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Nov 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jan 17, 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 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)23,4583
Polymers23,3241
Non-polymers1342
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.902, 58.453, 67.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-WOT / phenylazanium


Mass: 94.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8N
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: D2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, 16.5% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 2.667 Å
DetectorType: MAATEL BIODIFF / Detector: IMAGE PLATE / Date: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.667 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 38342 / % possible obs: 93.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.253
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.858 / % possible all: 82.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2429)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I8H

4i8h


Resolution: 1.43→22.09 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.86
RfactorNum. reflection% reflectionSelection details
Rfree0.1934 1911 4.99 %Random selection
Rwork0.1639 ---
obs0.1653 38317 93.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0053584
NEUTRON DIFFRACTIONf_angle_d1.0376129
NEUTRON DIFFRACTIONf_dihedral_angle_d13.596900
NEUTRON DIFFRACTIONf_chiral_restr0.086254
NEUTRON DIFFRACTIONf_plane_restr0.005782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4295-1.46530.29751220.26072279NEUTRON DIFFRACTION84
1.4653-1.50490.30341530.2422569NEUTRON DIFFRACTION95
1.5049-1.54920.26571490.2362617NEUTRON DIFFRACTION97
1.5492-1.59920.25751460.20662626NEUTRON DIFFRACTION96
1.5992-1.65630.19781350.18062628NEUTRON DIFFRACTION96
1.6563-1.72260.22681360.17432624NEUTRON DIFFRACTION95
1.7226-1.8010.19761330.16532577NEUTRON DIFFRACTION94
1.801-1.89590.18941360.15562592NEUTRON DIFFRACTION94
1.8959-2.01460.18811510.14372560NEUTRON DIFFRACTION93
2.0146-2.170.16871360.13382544NEUTRON DIFFRACTION92
2.17-2.38810.16331270.13492562NEUTRON DIFFRACTION92
2.3881-2.73310.15831330.14042676NEUTRON DIFFRACTION96
2.7331-3.44140.17931230.15662720NEUTRON DIFFRACTION95
3.4414-22.0930.14221310.14392832NEUTRON DIFFRACTION95

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