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

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Basic information

Entry
Database: PDB / ID: 5mos
TitleJoint X-ray/neutron structure of cationic trypsin in complex with N-amidinopiperidine
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
[azanyl(piperidin-1-yl)methylidene]azanium / DEUTERATED WATER / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsSchiebel, J. / Schrader, T.E. / Ostermann, A. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
European Research Council268145-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 14, 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 1.3May 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)23,5894
Polymers23,3241
Non-polymers2643
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19450 Å2
ΔGint22 kcal/mol
Surface area9630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.903, 58.646, 67.615
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-D86 / [azanyl(piperidin-1-yl)methylidene]azanium


Mass: 128.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N3
#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.: 171 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
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, 16.0-16.5% (w/v) PEG 8000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12951
22951
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)10.7749
NUCLEAR REACTORFRM II BIODIFF22.673, 2.678
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJun 10, 2015
MAATEL BIODIFF2IMAGE PLATEOct 9, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
10.77491
22.6731
32.6781
Reflection

Entry-ID: 5MOS

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rsym valueDiffraction-IDNet I/σ(I)
0.96-42.62113262899.48.6810.038128.43
1.5-503166588.73.10.1127.525
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
0.96-1.028.4120.5664.3198.9
1.5-1.532.60.4542.182279.9

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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

% reflection Rfree: 5.02 % / SU ML: 0.04 / R Free selection details: Random selection / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 6.54 / 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 obs (%)Diffraction-IDσ(F)
0.96-27.451X-RAY DIFFRACTION0.10440.09290.0934664813253999.411.36
1.5-22.152NEUTRON DIFFRACTION0.17960.16630.16715873162388.552
Refinement stepCycle: LAST / Resolution: 0.96→27.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 15 171 1798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073902
X-RAY DIFFRACTIONf_angle_d1.386663
X-RAY DIFFRACTIONf_dihedral_angle_d14.0471011
X-RAY DIFFRACTIONf_chiral_restr0.101281
X-RAY DIFFRACTIONf_plane_restr0.009797
NEUTRON DIFFRACTIONf_bond_d0.0073902
NEUTRON DIFFRACTIONf_angle_d1.386663
NEUTRON DIFFRACTIONf_dihedral_angle_d14.0471011
NEUTRON DIFFRACTIONf_chiral_restr0.101281
NEUTRON DIFFRACTIONf_plane_restr0.009797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9603-0.97120.17692090.16594089X-RAY DIFFRACTION98
0.9712-0.98260.16252260.15254155X-RAY DIFFRACTION99
0.9826-0.99460.12782150.14314141X-RAY DIFFRACTION99
0.9946-1.00720.1411910.13244167X-RAY DIFFRACTION99
1.0072-1.02040.13482390.11644144X-RAY DIFFRACTION99
1.0204-1.03440.12512180.10624161X-RAY DIFFRACTION100
1.0344-1.04920.08832270.0914167X-RAY DIFFRACTION100
1.0492-1.06480.10792280.08374104X-RAY DIFFRACTION99
1.0648-1.08150.09072400.07534125X-RAY DIFFRACTION99
1.0815-1.09920.07462000.06924180X-RAY DIFFRACTION100
1.0992-1.11820.06792210.06494143X-RAY DIFFRACTION99
1.1182-1.13850.07482230.06154135X-RAY DIFFRACTION99
1.1385-1.16040.06882480.05694188X-RAY DIFFRACTION100
1.1604-1.18410.07582220.06064158X-RAY DIFFRACTION100
1.1841-1.20980.07422200.06264211X-RAY DIFFRACTION99
1.2098-1.2380.0772330.06294133X-RAY DIFFRACTION100
1.238-1.26890.07762150.06274208X-RAY DIFFRACTION100
1.2689-1.30320.07682140.0644227X-RAY DIFFRACTION100
1.3032-1.34160.07712300.06554166X-RAY DIFFRACTION99
1.3416-1.38490.08731980.06574213X-RAY DIFFRACTION100
1.3849-1.43440.07332210.06814184X-RAY DIFFRACTION99
1.4344-1.49180.07912040.06694223X-RAY DIFFRACTION100
1.4918-1.55970.08122210.06954208X-RAY DIFFRACTION100
1.5597-1.64190.08452260.07064256X-RAY DIFFRACTION100
1.6419-1.74480.08092200.07534230X-RAY DIFFRACTION100
1.7448-1.87950.08722260.07974262X-RAY DIFFRACTION100
1.8795-2.06850.09612380.08154256X-RAY DIFFRACTION100
2.0685-2.36770.10942290.094268X-RAY DIFFRACTION99
2.3677-2.98250.11582260.11564308X-RAY DIFFRACTION99
2.9825-27.46270.15722200.13554481X-RAY DIFFRACTION99
1.4989-1.54730.26371210.29352383NEUTRON DIFFRACTION78
1.5473-1.60250.24131360.22492505NEUTRON DIFFRACTION83
1.6025-1.66670.23241260.19612604NEUTRON DIFFRACTION85
1.6667-1.74250.19551430.18692625NEUTRON DIFFRACTION86
1.7425-1.83430.18811500.17642690NEUTRON DIFFRACTION88
1.8343-1.94920.17571500.16312682NEUTRON DIFFRACTION88
1.9492-2.09960.18281440.15062729NEUTRON DIFFRACTION89
2.0996-2.31070.15881550.14282696NEUTRON DIFFRACTION88
2.3107-2.64460.14661450.14022823NEUTRON DIFFRACTION91
2.6446-3.33010.16621650.14863008NEUTRON DIFFRACTION96
3.3301-22.1540.15831520.1513291NEUTRON DIFFRACTION100

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