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- PDB-2r9p: Human mesotrypsin complexed with bovine pancreatic trypsin inhibi... -

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Basic information

Entry
Database: PDB / ID: 2r9p
TitleHuman mesotrypsin complexed with bovine pancreatic trypsin inhibitor(BPTI)
Components
  • Pancreatic trypsin inhibitor
  • Trypsin-3
Keywordshydrolase/hydrolase inhibitor / Human mesotrypsin / Serine protease / Bovine pancreatic trypsin inhibitor / BPTI / Alternative splicing / Calcium / Digestion / Hydrolase / Metal-binding / Secreted / Sulfation / Zymogen / Pharmaceutical / Protease inhibitor / Serine protease inhibitor / 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 / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / antimicrobial humoral response / Alpha-defensins / zymogen activation ...Uptake of dietary cobalamins into enterocytes / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / antimicrobial humoral response / Alpha-defensins / zymogen activation / Antimicrobial peptides / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / endothelial cell migration / trypsin / serine protease inhibitor complex / digestion / serine-type peptidase activity / serine-type endopeptidase inhibitor activity / tertiary granule lumen / protease binding / serine-type endopeptidase activity / calcium ion binding / Neutrophil degranulation / proteolysis / extracellular space / extracellular region
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 / Few Secondary Structures ...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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine 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 / Trypsin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSalameh, M.A. / Soares, A.S. / Radisky, E.S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural Basis for Accelerated Cleavage of Bovine Pancreatic Trypsin Inhibitor (BPTI) by Human Mesotrypsin.
Authors: Salameh, M.A. / Soares, A.S. / Hockla, A. / Radisky, E.S.
History
DepositionSep 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Trypsin-3
B: Trypsin-3
C: Trypsin-3
D: Trypsin-3
I: Pancreatic trypsin inhibitor
E: Pancreatic trypsin inhibitor
F: Pancreatic trypsin inhibitor
G: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,06128
Polymers123,1408
Non-polymers1,92120
Water11,403633
1
A: Trypsin-3
E: Pancreatic trypsin inhibitor
hetero molecules

C: Trypsin-3
G: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,33912
Polymers61,5704
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_454x-1,y,z-11
identity operation1_555x,y,z1
Buried area5650 Å2
MethodPISA
2
B: Trypsin-3
F: Pancreatic trypsin inhibitor
hetero molecules

D: Trypsin-3
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,72316
Polymers61,5704
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area6790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.222, 109.717, 81.171
Angle α, β, γ (deg.)90.00, 117.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Trypsin-3 / Trypsin III / Brain trypsinogen / Mesotrypsinogen / Trypsin IV / Serine protease 3 / Serine protease 4


Mass: 24257.457 Da / Num. of mol.: 4 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS3, PRSS4, TRY3, TRY4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P35030, trypsin
#2: Protein
Pancreatic trypsin inhibitor / Basic protease inhibitor / BPI / BPTI / Aprotinin


Mass: 6527.568 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Strain: A1153 / References: UniProt: P00974
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 1.6M ammonium sulfate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 221478 / % possible obs: 97.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 18.803 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 15.275
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.84 / % possible all: 96.2

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Processing

Software
NameClassification
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1H4W and 2PTC

1h4w

2ptc


Resolution: 1.4→25.6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 --The free R set was chosen as to fit the symmetry of the lattice, avoiding the mixing of work and free reflections mixing in due to possible twin relations.
Rwork0.1695 ---
all0.1704 ---
obs0.1704 221478 98.4 %-
Displacement parametersBiso mean: 18.8 Å2
Refinement stepCycle: LAST / Resolution: 1.4→25.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8665 0 105 644 9414
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg0.914
LS refinement shellResolution: 1.4→1.45 Å

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