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- PDB-5mnc: Cationic trypsin in complex with aniline (deuterated sample at 100 K) -

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Basic information

Entry
Database: PDB / ID: 5mnc
TitleCationic trypsin in complex with aniline (deuterated sample at 100 K)
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
ANILINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.916 Å
AuthorsSchiebel, J. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind Germany
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 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _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
Revision 1.3Nov 13, 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)23,9388
Polymers23,3241
Non-polymers6147
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-66 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.590, 58.224, 66.700
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ANL / ANILINE


Mass: 93.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.87 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.7069 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7069 Å / Relative weight: 1
ReflectionResolution: 0.916→42.245 Å / Num. obs: 146365 / % possible obs: 97.9 % / Redundancy: 6.507 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 18.82
Reflection shellResolution: 0.916→0.97 Å / Redundancy: 6.13 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.74 / % possible all: 94.6

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Processing

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

4i8h


Resolution: 0.916→14.291 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 9.85
RfactorNum. reflection% reflectionSelection details
Rfree0.1216 7314 5 %Random selection
Rwork0.1071 ---
obs0.1078 146285 97.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.916→14.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 33 335 1991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092018
X-RAY DIFFRACTIONf_angle_d1.1812792
X-RAY DIFFRACTIONf_dihedral_angle_d14.357760
X-RAY DIFFRACTIONf_chiral_restr0.099296
X-RAY DIFFRACTIONf_plane_restr0.009381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9159-0.92630.23872110.23683999X-RAY DIFFRACTION85
0.9263-0.93720.20932390.18684546X-RAY DIFFRACTION97
0.9372-0.94860.16952380.16824509X-RAY DIFFRACTION97
0.9486-0.96060.1772400.15384562X-RAY DIFFRACTION97
0.9606-0.97320.15512410.14294584X-RAY DIFFRACTION97
0.9732-0.98660.13532390.13124549X-RAY DIFFRACTION98
0.9866-1.00070.15472410.12644585X-RAY DIFFRACTION98
1.0007-1.01560.15662390.12254543X-RAY DIFFRACTION97
1.0156-1.03150.13232360.11444494X-RAY DIFFRACTION96
1.0315-1.04840.11972420.10624606X-RAY DIFFRACTION98
1.0484-1.06640.1092430.09754626X-RAY DIFFRACTION98
1.0664-1.08580.10642420.0964594X-RAY DIFFRACTION99
1.0858-1.10670.10452460.09234674X-RAY DIFFRACTION99
1.1067-1.12930.09392430.08474599X-RAY DIFFRACTION99
1.1293-1.15380.08962440.08184651X-RAY DIFFRACTION99
1.1538-1.18070.1032460.08484667X-RAY DIFFRACTION99
1.1807-1.21020.10872450.08514657X-RAY DIFFRACTION99
1.2102-1.24290.09882450.08484644X-RAY DIFFRACTION99
1.2429-1.27940.09762440.0874646X-RAY DIFFRACTION99
1.2794-1.32070.09972450.09084659X-RAY DIFFRACTION99
1.3207-1.36790.11682450.09414664X-RAY DIFFRACTION99
1.3679-1.42260.1012450.09064649X-RAY DIFFRACTION98
1.4226-1.48730.11222490.0894734X-RAY DIFFRACTION100
1.4873-1.56560.11922490.08694717X-RAY DIFFRACTION100
1.5656-1.66350.10522500.0944756X-RAY DIFFRACTION100
1.6635-1.79170.11912490.09844735X-RAY DIFFRACTION100
1.7917-1.97160.1362510.10764780X-RAY DIFFRACTION100
1.9716-2.2560.11682530.10574796X-RAY DIFFRACTION100
2.256-2.83860.1272520.11884789X-RAY DIFFRACTION99
2.8386-14.2930.13272620.12354957X-RAY DIFFRACTION98

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