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- PDB-5mo0: Neutron structure of cationic trypsin in complex with benzamidine -

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Basic information

Entry
Database: PDB / ID: 5mo0
TitleNeutron structure of cationic trypsin in complex with benzamidine
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
BENZAMIDINE / DEUTERATED WATER / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsSchiebel, J. / Schrader, T.E. / Ostermann, A. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind268145-DrugProfilBind
CitationJournal: Nat Commun / Year: 2018
Title: Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes.
Authors: Schiebel, J. / Gaspari, R. / Wulsdorf, T. / Ngo, K. / Sohn, C. / Schrader, T.E. / Cavalli, A. / Ostermann, A. / Heine, A. / Klebe, G.
History
DepositionDec 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site
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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.pdbx_formal_charge / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jan 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 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)23,4853
Polymers23,3241
Non-polymers1602
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.912, 58.686, 67.516
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-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 144 / 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, 13% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 2.673 Å
DetectorType: MAATEL BIODIFF / Detector: IMAGE PLATE / Date: Sep 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.673 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 31713 / % possible obs: 89.4 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.197
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 3.244 / % possible all: 69.6

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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: 1.502→25.433 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.96
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1573 4.96 %Random selection
Rwork0.147 ---
obs0.1489 31693 89.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0043696
NEUTRON DIFFRACTIONf_angle_d0.9456306
NEUTRON DIFFRACTIONf_dihedral_angle_d11.7911341
NEUTRON DIFFRACTIONf_chiral_restr0.06260
NEUTRON DIFFRACTIONf_plane_restr0.005796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5022-1.55070.27391250.22242101NEUTRON DIFFRACTION71
1.5507-1.60610.24321380.18372431NEUTRON DIFFRACTION81
1.6061-1.67040.23311390.16812573NEUTRON DIFFRACTION85
1.6704-1.74640.19471220.15282694NEUTRON DIFFRACTION89
1.7464-1.83850.21041650.1492744NEUTRON DIFFRACTION91
1.8385-1.95360.18421550.14122824NEUTRON DIFFRACTION93
1.9536-2.10440.17791530.12952870NEUTRON DIFFRACTION94
2.1044-2.3160.16771360.12392756NEUTRON DIFFRACTION90
2.316-2.65080.14131500.12622896NEUTRON DIFFRACTION94
2.6508-3.33860.15681370.15263093NEUTRON DIFFRACTION98
3.3386-25.43710.17141530.14323138NEUTRON DIFFRACTION96

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