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- PDB-7ph1: Trypsin in complex with BPTI mutant (2S)-2-amino-4-monofluorobuta... -

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Basic information

Entry
Database: PDB / ID: 7ph1
TitleTrypsin in complex with BPTI mutant (2S)-2-amino-4-monofluorobutanoic acid
Components
  • Cationic trypsin
  • Pancreatic trypsin inhibitor
KeywordsHYDROLASE / HYDROLASE INHIBITORS / METAL-BINDING / SERINE PROTEASE / HYDROLASE-2 INHIBITOR COMPLEX
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family ...Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Serine protease 1 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsDimos, N. / Leppkes, J. / Koksch, B. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SfB 1349 / 387284271 Germany
Citation
Journal: J.Phys.Chem.B / Year: 2022
Title: Water Network in the Binding Pocket of Fluorinated BPTI-Trypsin Complexes─Insights from Simulation and Experiment.
Authors: Wehrhan, L. / Leppkes, J. / Dimos, N. / Loll, B. / Koksch, B. / Keller, B.G.
#1: Journal: Biorxiv / Year: 2022
Title: Water Network in the Binding Pocket of Fluorinated BPTI-Trypsin Complexes - Insights from Simulation and Experiment
Authors: Wehrhan, L. / Leppkes, J. / Dimos, N. / Loll, B. / Koksch, B. / Keller, B.G.
#2: Journal: Chem Sci / Year: 2015
Title: Fluorine teams up with water to restore inhibitor activity to mutant BPTI
Authors: Ye, S. / Loll, B. / Berger, A.A. / Muelow, U. / Alings, C. / Wahl, M.C. / Koksch, B.
History
DepositionAug 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / citation_author
Revision 1.3Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Cationic trypsin
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,78625
Polymers29,6692
Non-polymers2,11823
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-187 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.975, 81.289, 124.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 2 molecules EI

#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: Protein Pancreatic trypsin inhibitor / Aprotinin / Basic protease inhibitor / BPI / BPTI


Mass: 6344.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P00974

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Non-polymers , 4 types, 345 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 17, 2020
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.18→30 Å / Num. obs: 124357 / % possible obs: 99.8 % / Redundancy: 7.4 % / CC1/2: 0.99 / Rrim(I) all: 0.093 / Net I/σ(I): 10.02
Reflection shellResolution: 1.18→1.21 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 0.91 / Num. unique obs: 19736 / CC1/2: 0.456 / Rrim(I) all: 2.049 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y11

4y11


Resolution: 1.18→27.56 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1659 1810 1.46 %
Rwork0.149 122410 -
obs0.1492 124220 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.64 Å2 / Biso mean: 23.9511 Å2 / Biso min: 10.78 Å2
Refinement stepCycle: final / Resolution: 1.18→27.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 225 322 2617
Biso mean--40.64 32.89 -
Num. residues----280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.18-1.210.35891500.342993079457
1.21-1.250.3021460.322793399485
1.25-1.290.39921220.308393539475
1.29-1.330.26211470.264693409487
1.33-1.390.27411330.216693629495
1.39-1.450.20151400.184693509490
1.45-1.530.18321370.157793659502
1.53-1.620.16341390.136293899528
1.62-1.750.11861370.109594099546
1.75-1.920.13761410.109594269567
1.92-2.20.13321310.108794679598
2.2-2.770.12851410.13195349675
2.77-27.560.16631460.149897699915

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