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- PDB-5moo: Joint X-ray/neutron structure of cationic trypsin in complex with... -

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Basic information

Entry
Database: PDB / ID: 5moo
TitleJoint X-ray/neutron 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 / 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 / phenylazanium / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.441 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 14, 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 2.2May 1, 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

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5554
Polymers23,3241
Non-polymers2303
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17960 Å2
ΔGint19 kcal/mol
Surface area8900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.875, 58.472, 67.458
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-WOT / phenylazanium / Aniline


Mass: 94.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8N
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.98 %
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, 16.5-17.0% (w/v) PEG 8000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12951
22951
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SEALED TUBEOTHER11.54179
NUCLEAR REACTORFRM II BIODIFF22.667
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATEFeb 19, 2016
MAATEL BIODIFF2IMAGE PLATEJul 22, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541791
22.6671
Reflection

Entry-ID: 5MOO

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.441-44.1843879397.37.3610.045127.01
1.43-503834293.82.50.09827.253
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.441-1.536.0250.2299.86184.6
1.43-1.451.60.3871.858282.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2429)refinement
XDSdata reduction
HKL-2000data reduction
XDSdata scaling
HKL-2000data scaling
PHASERphasing
Cootmodel building
Refinement

SU ML: 0.25 / R Free selection details: Random selection / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 17.11 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 4I8H

4i8h

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.441-44.184X-RAY DIFFRACTION0.15960.13440.13571959387765.0597.2811.36
1.43-22.092NEUTRON DIFFRACTION0.18480.170.17081911383174.9993.792
Refinement stepCycle: LAST / Resolution: 1.441→44.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 13 149 1772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063758
X-RAY DIFFRACTIONf_angle_d1.0856417
X-RAY DIFFRACTIONf_dihedral_angle_d12.911976
X-RAY DIFFRACTIONf_chiral_restr0.093270
X-RAY DIFFRACTIONf_plane_restr0.006790
NEUTRON DIFFRACTIONf_bond_d0.0063758
NEUTRON DIFFRACTIONf_angle_d1.0856417
NEUTRON DIFFRACTIONf_dihedral_angle_d12.911976
NEUTRON DIFFRACTIONf_chiral_restr0.093270
NEUTRON DIFFRACTIONf_plane_restr0.006790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4415-1.47750.66011140.66381785X-RAY DIFFRACTION68
1.4775-1.51750.28711520.2932614X-RAY DIFFRACTION98
1.5175-1.56210.26121350.21522598X-RAY DIFFRACTION98
1.5621-1.61260.16221580.10862650X-RAY DIFFRACTION99
1.6126-1.67020.14551400.08382661X-RAY DIFFRACTION100
1.6702-1.73710.11250.07372659X-RAY DIFFRACTION100
1.7371-1.81610.11961540.07722687X-RAY DIFFRACTION100
1.8161-1.91190.11441470.08042678X-RAY DIFFRACTION100
1.9119-2.03170.11621550.08092675X-RAY DIFFRACTION100
2.0317-2.18850.10541460.08562694X-RAY DIFFRACTION100
2.1885-2.40870.12141330.09092716X-RAY DIFFRACTION100
2.4087-2.75720.13781400.11352748X-RAY DIFFRACTION100
2.7572-3.47360.14751230.1262785X-RAY DIFFRACTION100
3.4736-44.20470.11051370.11422867X-RAY DIFFRACTION99
1.4292-1.46490.28661230.26662266NEUTRON DIFFRACTION84
1.4649-1.50450.29861500.24882569NEUTRON DIFFRACTION95
1.5045-1.54880.26671500.26012617NEUTRON DIFFRACTION97
1.5488-1.59870.2351450.22242628NEUTRON DIFFRACTION96
1.5987-1.65590.21231380.19692635NEUTRON DIFFRACTION96
1.6559-1.72210.21251360.18372622NEUTRON DIFFRACTION95
1.7221-1.80050.18741320.17942580NEUTRON DIFFRACTION94
1.8005-1.89540.17561360.16932594NEUTRON DIFFRACTION94
1.8954-2.0140.16871510.15022553NEUTRON DIFFRACTION93
2.014-2.16940.15251360.14322546NEUTRON DIFFRACTION93
2.1694-2.38750.1571270.13782562NEUTRON DIFFRACTION92
2.3875-2.73240.1461330.13472682NEUTRON DIFFRACTION96
2.7324-3.44050.16841230.15062719NEUTRON DIFFRACTION95
3.4405-22.09460.14561310.14622833NEUTRON DIFFRACTION95

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