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- PDB-5mnf: Cationic trypsin in its apo form (deuterated sample at 295 K) -

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Basic information

Entry
Database: PDB / ID: 5mnf
TitleCationic trypsin in its apo form (deuterated sample at 295 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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsSchiebel, J. / 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 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 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 1.2Jan 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 20, 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)23,4603
Polymers23,3241
Non-polymers1362
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-25 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.999, 58.623, 67.565
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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
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% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.7749 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: 0.7749 Å / Relative weight: 1
ReflectionResolution: 0.99→44.279 Å / Num. obs: 121717 / % possible obs: 99.8 % / Redundancy: 8.681 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 27.03
Reflection shellResolution: 0.99→1.05 Å / Redundancy: 8.29 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 4.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I8H

4i8h


Resolution: 0.99→19.226 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 7.04
RfactorNum. reflection% reflectionSelection details
Rfree0.107 6080 5 %Random selection
Rwork0.0961 ---
obs0.0967 121609 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.99→19.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 6 184 1797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081846
X-RAY DIFFRACTIONf_angle_d1.0812555
X-RAY DIFFRACTIONf_dihedral_angle_d11.629673
X-RAY DIFFRACTIONf_chiral_restr0.1281
X-RAY DIFFRACTIONf_plane_restr0.009341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.99-1.00120.21561980.19223760X-RAY DIFFRACTION98
1.0012-1.0130.18651990.16843780X-RAY DIFFRACTION100
1.013-1.02540.16232000.153809X-RAY DIFFRACTION100
1.0254-1.03830.1822020.1383829X-RAY DIFFRACTION100
1.0383-1.0520.13591990.11613782X-RAY DIFFRACTION100
1.052-1.06640.11962010.10763823X-RAY DIFFRACTION100
1.0664-1.08160.10952010.09743808X-RAY DIFFRACTION100
1.0816-1.09780.10632010.0893813X-RAY DIFFRACTION100
1.0978-1.11490.10462020.07943853X-RAY DIFFRACTION100
1.1149-1.13320.08022010.07823815X-RAY DIFFRACTION100
1.1332-1.15280.08812000.0713803X-RAY DIFFRACTION100
1.1528-1.17370.07272010.0743829X-RAY DIFFRACTION100
1.1737-1.19630.0922020.07663846X-RAY DIFFRACTION100
1.1963-1.22070.0782030.07013839X-RAY DIFFRACTION100
1.2207-1.24720.08092010.06693815X-RAY DIFFRACTION100
1.2472-1.27620.07222020.06343850X-RAY DIFFRACTION100
1.2762-1.30820.07112010.06573816X-RAY DIFFRACTION100
1.3082-1.34350.08682030.0683847X-RAY DIFFRACTION100
1.3435-1.3830.07562020.07093852X-RAY DIFFRACTION100
1.383-1.42770.08042010.07223820X-RAY DIFFRACTION100
1.4277-1.47870.09252040.073872X-RAY DIFFRACTION100
1.4787-1.53790.08322030.06913870X-RAY DIFFRACTION100
1.5379-1.60780.07762030.06963856X-RAY DIFFRACTION100
1.6078-1.69250.08472050.07673874X-RAY DIFFRACTION100
1.6925-1.79850.09582030.08173861X-RAY DIFFRACTION100
1.7985-1.93720.09612050.08653907X-RAY DIFFRACTION100
1.9372-2.1320.09362050.08713899X-RAY DIFFRACTION100
2.132-2.43990.10142070.10043936X-RAY DIFFRACTION100
2.4399-3.0720.13382100.12423973X-RAY DIFFRACTION100
3.072-19.22960.14132150.1214092X-RAY DIFFRACTION99

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