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- PDB-4wxv: Human cationic trypsin K97D mutant in complex with bovine pancrea... -

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Basic information

Entry
Database: PDB / ID: 4wxv
TitleHuman cationic trypsin K97D mutant in complex with bovine pancreatic trypsin inhibitor (BPTI)
Components
  • Pancreatic trypsin inhibitor
  • Trypsin-1
KeywordsHydrolase/Hydrolase Inhibitor / trypsin inhibitor / 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 / zymogen binding / Developmental Lineage of Pancreatic Acinar Cells / 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 / zymogen binding / Developmental Lineage of Pancreatic Acinar Cells / 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: 2.1 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 14, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.7Oct 23, 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: Trypsin-1
B: Trypsin-1
C: Pancreatic trypsin inhibitor
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,32510
Polymers60,8614
Non-polymers4646
Water1,35175
1
A: Trypsin-1
C: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6635
Polymers30,4302
Non-polymers2323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-32 kcal/mol
Surface area11880 Å2
MethodPISA
2
B: Trypsin-1
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6635
Polymers30,4302
Non-polymers2323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-59 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.853, 56.575, 228.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24088.062 Da / Num. of mol.: 2 / Fragment: UNP residues 24-247 / Mutation: K97D, R117H, S195A
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: 6342.387 Da / Num. of mol.: 2 / Fragment: UNP residues 36-90
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1 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: 2.1→38.1 Å / Num. obs: 32877 / % possible obs: 98.1 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.9
Reflection shellHighest resolution: 2.1 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 4.24 / % possible all: 85.3

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Processing

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

2ra3


Resolution: 2.1→38.1 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.898 / SU B: 5.945 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2809 1665 5.1 %RANDOM
Rwork0.2157 31212 --
obs0.219 31212 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.61 Å2 / Biso mean: 25.878 Å2 / Biso min: 12.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0 Å2
2---0.11 Å2-0 Å2
3---0.36 Å2
Refinement stepCycle: final / Resolution: 2.1→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3816 0 22 76 3914
Biso mean--56.23 21 -
Num. residues----558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194373
X-RAY DIFFRACTIONr_bond_other_d0.0010.024054
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.9485941
X-RAY DIFFRACTIONr_angle_other_deg0.8633.0079293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8945554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99724.479192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75215693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3051522
X-RAY DIFFRACTIONr_chiral_restr0.1060.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021022
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 105 -
Rwork0.247 1909 -
all-2014 -
obs--82.47 %

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