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- PDB-4wwy: human cationic trypsin G193R mutant in complex with bovine pancre... -

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Basic information

Entry
Database: PDB / ID: 4wwy
Titlehuman cationic trypsin G193R mutant in complex with bovine pancreatic trypsin inhibitor
Components
  • Pancreatic trypsin inhibitor
  • Trypsin-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / trypsin inhibitors / complex / BPTI / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Uptake of dietary cobalamins into enterocytes / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / Developmental Lineage of Pancreatic Acinar Cells / zymogen binding / molecular function inhibitor activity / Activation of Matrix Metalloproteinases ...Uptake of dietary cobalamins into enterocytes / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / Developmental Lineage of Pancreatic Acinar Cells / zymogen binding / molecular function inhibitor activity / Activation of Matrix Metalloproteinases / negative regulation of thrombin-activated receptor signaling pathway / extracellular matrix disassembly / trypsin / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / : / blood microparticle / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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 ...: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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 / : / Few Secondary Structures / Irregular / 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
Pancreatic trypsin inhibitor / Serine protease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAlloy, A. / Kayode, O. / Soares, A.S. / Wang, R. / Radisky, E.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA154387 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Mesotrypsin Has Evolved Four Unique Residues to Cleave Trypsin Inhibitors as Substrates.
Authors: Alloy, A.P. / Kayode, O. / Wang, R. / Hockla, A. / Soares, A.S. / Radisky, E.S.
History
DepositionNov 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Experimental preparation
Revision 1.3Sep 9, 2015Group: Database references
Revision 1.4Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: 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 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypsin-1
B: Trypsin-1
C: Pancreatic trypsin inhibitor
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,30013
Polymers61,4924
Non-polymers8099
Water7,026390
1
A: Trypsin-1
C: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2267
Polymers30,7462
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-70 kcal/mol
Surface area12600 Å2
MethodPISA
2
B: Trypsin-1
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0746
Polymers30,7462
Non-polymers3284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-70 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.952, 63.227, 90.535
Angle α, β, γ (deg.)90.000, 94.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Trypsin-1 / Beta-trypsin / Cationic trypsinogen / Serine protease 1 / Trypsin I


Mass: 24218.297 Da / Num. of mol.: 2 / Fragment: UNP residues 24-247 / Mutation: G193R, R117H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS1, TRP1, TRY1, TRYP1 / Organ: pancreas / Plasmid: pTRAP-T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07477, trypsin
#2: Protein Pancreatic trypsin inhibitor / Aprotinin / Basic protease inhibitor / BPTI


Mass: 6527.568 Da / Num. of mol.: 2 / Fragment: UNP residues 36-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: Pancreas / Plasmid: pPICZa / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P00974
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M sodium cacodylate trihydrate, 30% PEG-8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Feb 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→47.29 Å / Num. obs: 59179 / % possible obs: 89.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 17
Reflection shellHighest resolution: 1.7 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 1.21 / % possible all: 45.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RA3

2ra3


Resolution: 1.7→47.29 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.13 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 3029 5.1 %RANDOM
Rwork0.1708 56150 --
obs0.1727 59179 89.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.31 Å2 / Biso mean: 19.323 Å2 / Biso min: 5.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20.03 Å2
2---0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.7→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4283 0 51 399 4733
Biso mean--44.38 26.38 -
Num. residues----564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194488
X-RAY DIFFRACTIONr_bond_other_d0.0010.024147
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9596108
X-RAY DIFFRACTIONr_angle_other_deg0.9023.0079515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6595576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77924.564195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64215719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8871524
X-RAY DIFFRACTIONr_chiral_restr0.1230.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021045
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 108 -
Rwork0.35 2157 -
all-2265 -
obs--46.83 %

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