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- PDB-3p92: Human mesotrypsin complexed with bovine pancreatic trypsin inhibi... -

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Basic information

Entry
Database: PDB / ID: 3p92
TitleHuman mesotrypsin complexed with bovine pancreatic trypsin inhibitor variant (BPTI-K15R/R17G)
Components
  • PRSS3 protein
  • Pancreatic trypsin inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / mesotrypsin / trypsin IV / canonical inhibitor / bovine pancreatic trypsin inibitor / 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 / 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: 1.5992 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 1.2Oct 8, 2014Group: Structure summary
Revision 1.3Sep 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_asym_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_asym_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 1.4Oct 30, 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)30,7533
Polymers30,7132
Non-polymers401
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PRSS3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2982
Polymers24,2571
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)6,4551
Polymers6,4551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.282, 39.222, 68.807
Angle α, β, γ (deg.)90.000, 100.280, 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) / References: UniProt: Q8N2U3, UniProt: P35030*PLUS, trypsin
#2: Protein Pancreatic trypsin inhibitor / Aprotinin / Basic protease inhibitor / BPI / BPTI


Mass: 6455.440 Da / Num. of mol.: 1 / Fragment: UNP Residues 36-93 / Mutation: K15R, R17G
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.: 299 / 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: 1.91 Å3/Da / Density % sol: 35.75 %
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: 1.599→33.851 Å / Num. all: 27380 / Num. obs: 27380 / % possible obs: 88.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 7.48 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 39.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2r9p


Resolution: 1.5992→33.851 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9196 / SU ML: 0.13 / σ(F): 0.18 / Phase error: 14.17 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1586 2000 7.3 %
Rwork0.1113 --
obs0.1148 27380 88.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.39 Å2 / ksol: 0.477 e/Å3
Displacement parametersBiso max: 113.53 Å2 / Biso mean: 15.889 Å2 / Biso min: 3.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.8586 Å2-0 Å20.1939 Å2
2---0.7699 Å2-0 Å2
3----1.6904 Å2
Refinement stepCycle: LAST / Resolution: 1.5992→33.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 1 299 2450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074328
X-RAY DIFFRACTIONf_angle_d0.9077781
X-RAY DIFFRACTIONf_chiral_restr0.078327
X-RAY DIFFRACTIONf_plane_restr0.004695
X-RAY DIFFRACTIONf_dihedral_angle_d16.4611072
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 (%)
1.5992-1.63920.1432780.0822988106648
1.6392-1.68350.1883900.08111147123757
1.6835-1.7330.16431130.08361423153669
1.733-1.7890.14591310.0871664179581
1.789-1.85290.15641480.0941896204493
1.8529-1.92710.16281610.09932028218999
1.9271-2.01480.14851590.09432018217799
2.0148-2.1210.15481590.09220262185100
2.121-2.25390.14621620.094420522214100
2.2539-2.42780.16491610.10120532214100
2.4278-2.67210.14531620.104920522214100
2.6721-3.05850.17581620.121320482210100
3.0585-3.85250.15061560.11391985214195
3.8525-33.85860.16551580.15062000215894

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