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- PDB-5mo1: Neutron structure of cationic trypsin in complex with benzylamine -

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Basic information

Entry
Database: PDB / ID: 5mo1
TitleNeutron structure of cationic trypsin in complex with benzylamine
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...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. / Serine proteases, trypsin family, serine active site. / 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 / (phenylmethyl)azanium / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.491 Å
AuthorsSchiebel, J. / Schrader, T.E. / Ostermann, A. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind
CitationJournal: to be published
Title: Neutron structure of cationic trypsin in complex with benzylamine
Authors: Schiebel, J. / Heine, A. / Klebe, G.
History
DepositionDec 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 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

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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)23,4733
Polymers23,3241
Non-polymers1482
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.017, 58.630, 67.753
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 (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-UFZ / (phenylmethyl)azanium


Mass: 108.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10N
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: D2O

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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, 15% (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: Aug 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.673 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 34022 / % possible obs: 93.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 5.866
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.954 / % possible all: 90.4

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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: 1.491→19.68 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.81
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1713 5.04 %Random selection
Rwork0.1754 ---
obs0.1775 34004 93.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0053493
NEUTRON DIFFRACTIONf_angle_d1.0545939
NEUTRON DIFFRACTIONf_dihedral_angle_d14.6877
NEUTRON DIFFRACTIONf_chiral_restr0.087254
NEUTRON DIFFRACTIONf_plane_restr0.006776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4912-1.5350.30861490.26232424NEUTRON DIFFRACTION86
1.535-1.58460.26361480.22532682NEUTRON DIFFRACTION95
1.5846-1.64120.24211440.21332747NEUTRON DIFFRACTION96
1.6412-1.70680.24991480.19712754NEUTRON DIFFRACTION97
1.7068-1.78450.24361370.18932812NEUTRON DIFFRACTION98
1.7845-1.87850.23831550.18192768NEUTRON DIFFRACTION98
1.8785-1.99610.2431630.17022745NEUTRON DIFFRACTION97
1.9961-2.150.20741410.15982736NEUTRON DIFFRACTION95
2.15-2.3660.2171260.16542379NEUTRON DIFFRACTION82
2.366-2.70770.17611360.15572570NEUTRON DIFFRACTION89
2.7077-3.40850.17971250.15882761NEUTRON DIFFRACTION93
3.4085-19.68210.1631410.14562913NEUTRON DIFFRACTION95

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