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- PDB-3p95: Human mesotrypsin complexed with bovine pancreatic trypsin inhibi... -

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Basic information

Entry
Database: PDB / ID: 3p95
TitleHuman mesotrypsin complexed with bovine pancreatic trypsin inhibitor variant (BPTI-K15R/R17D)
Components
  • PRSS3 protein
  • Pancreatic trypsin inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Human mesotrypsin-canonical inhibitor complex / Mesotrypsin / Trypsin IV / Bovine Pancreatic Trypsin Inhibitor / canonical inhibitor / BPTI-K15R/R17D / 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 / antimicrobial humoral response / Alpha-defensins / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin ...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 / antimicrobial humoral response / Alpha-defensins / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / zymogen activation / Antimicrobial peptides / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / endothelial cell migration / 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 / 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, histidine active site. / Peptidase S1A, chymotrypsin family / 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 / trypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2991 Å
AuthorsSalameh, M.A. / Soares, A.S. / Radisky, E.S.
CitationJournal: Biochem.J. / Year: 2011
Title: The P2' residue is a key determinant of mesotrypsin specificity: engineering a high-affinity inhibitor with anticancer activity.
Authors: Salameh, M.A. / Soares, A.S. / Hockla, A. / Radisky, D.C. / Radisky, E.S.
History
DepositionOct 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Sep 6, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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: PRSS3 protein
E: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8113
Polymers30,7712
Non-polymers401
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-18 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.915, 39.095, 68.460
Angle α, β, γ (deg.)90.000, 100.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PRSS3 protein


Mass: 24257.457 Da / Num. of mol.: 1 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N2U3, UniProt: P35030*PLUS, trypsin
#2: Protein Pancreatic trypsin inhibitor / Aprotinin / Basic protease inhibitor / BPI / BPTI


Mass: 6513.476 Da / Num. of mol.: 1 / Fragment: UNP Residues 36-93 / Mutation: K15R, R17D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P00974
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 280 / 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: 1.88 Å3/Da / Density % sol: 34.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG4000, 0.2M Na acetate and 100mM Tris pH 8.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.299→50 Å / Num. obs: 53441 / % possible obs: 94.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.068 / Χ2: 1.21 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.299-1.323.80.2276.518041.24965
1.32-1.354.30.2120281.30771.7
1.35-1.374.50.20122801.30980.7
1.37-1.450.18525651.38591.3
1.4-1.4360.17127351.36597.1
1.43-1.466.10.15627651.37298.1
1.46-1.56.10.1427631.32198.9
1.5-1.546.20.12827811.32598.9
1.54-1.596.30.11627821.29499
1.59-1.646.40.10528121.25699.4
1.64-1.76.60.09928041.25799.4
1.7-1.766.80.09228031.26699.4
1.76-1.8470.08728141.25399.7
1.84-1.947.10.0828131.23299.9
1.94-2.067.20.07328291.18599.9
2.06-2.227.20.06928361.11899.9
2.22-2.457.20.06528581.07999.8
2.45-2.87.20.06228461.07499.9
2.8-3.536.70.05728220.94899
3.53-506.60.05727010.89591.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2008_09_13_0905phasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R9P

2r9p


Resolution: 1.2991→33.817 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9487 / SU ML: 0.07 / σ(F): 0.06 / Phase error: 10.34 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1319 2000 3.79 %
Rwork0.1105 --
obs0.1114 52821 93.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.547 Å2 / ksol: 0.485 e/Å3
Displacement parametersBiso max: 119.66 Å2 / Biso mean: 19.2292 Å2 / Biso min: 6.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.1026 Å20 Å20.4692 Å2
2--0.9199 Å2-0 Å2
3----3.6118 Å2
Refinement stepCycle: LAST / Resolution: 1.2991→33.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 1 280 2434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164349
X-RAY DIFFRACTIONf_angle_d1.3357818
X-RAY DIFFRACTIONf_chiral_restr0.13334
X-RAY DIFFRACTIONf_plane_restr0.009699
X-RAY DIFFRACTIONf_dihedral_angle_d16.6341087
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2991-1.33160.1605950.1062403249862
1.3316-1.36760.14851110.0972842295374
1.3676-1.40780.11991360.08963452358889
1.4078-1.45330.1191460.08213706385296
1.4533-1.50520.11881490.08193769391897
1.5052-1.56550.12571490.07753788393798
1.5655-1.63670.11311500.07713835398599
1.6367-1.7230.10071510.07823811396299
1.723-1.83090.11671520.08513882403499
1.8309-1.97230.1181530.089238634016100
1.9723-2.17070.11311530.087238914044100
2.1707-2.48480.12721530.099138944047100
2.4848-3.13020.14031540.117439294083100
3.1302-33.82820.14491480.15353756390493

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