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- PDB-3fp7: Anionic trypsin variant S195A in complex with bovine pancreatic t... -

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Basic information

Entry
Database: PDB / ID: 3fp7
TitleAnionic trypsin variant S195A in complex with bovine pancreatic trypsin inhibitor (BPTI) cleaved at the scissile bond (LYS15-ALA16) determined to the 1.46 A resolution limit
Components
  • (Pancreatic trypsin ...) x 2
  • Anionic trypsin-2
KeywordsHydrolase/Hydrolase inhibitor / ENZYME-INHIBITOR COMPLEX / PEPTIDE BOND HYDROLYSIS / Calcium / Digestion / Hydrolase / Metal-binding / Protease / Secreted / Serine protease / Zymogen / Pharmaceutical / Protease inhibitor / Serine protease inhibitor / Hydrolase-Hydrolase inhibitor COMPLEX
Function / homology
Function and homology information


Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / Neutrophil degranulation ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / Neutrophil degranulation / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / collagen catabolic process / trypsin / serine protease inhibitor complex / digestion / response to nutrient / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / calcium ion binding / 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 ...: / 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
Anionic trypsin-2 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsZakharova, E. / Horvath, M.P. / Goldenberg, D.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of a serine protease poised to resynthesize a peptide bond.
Authors: Zakharova, E. / Horvath, M.P. / Goldenberg, D.P.
History
DepositionJan 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_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 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 16, 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
E: Anionic trypsin-2
I: Pancreatic trypsin inhibitor
J: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,27314
Polymers30,3443
Non-polymers92911
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.969, 91.969, 61.001
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11E-806-

HOH

21E-809-

HOH

31E-843-

HOH

DetailsAUTHORS STATE THAT THE QUATERNARY STRUCTURE IS A HETEROTRIMER.

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Components

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Protein , 1 types, 1 molecules E

#1: Protein Anionic trypsin-2 / Anionic trypsin II / Pretrypsinogen II / Serine protease 2


Mass: 23798.838 Da / Num. of mol.: 1 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prss2, Try2 / Plasmid: PYT / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): DLM101 / References: UniProt: P00763, trypsin

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Pancreatic trypsin ... , 2 types, 2 molecules IJ

#2: Protein/peptide Pancreatic trypsin inhibitor / Basic protease inhibitor / BPTI / BPI / Aprotinin


Mass: 1724.996 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: bovine pancreatic trypsin inhibitor was obtained in its hydrolyzed form by partial reduction at the cys14-cys38 disulfide, treatment with trypsin, purification by HPLC and re-oxidation of ...Details: bovine pancreatic trypsin inhibitor was obtained in its hydrolyzed form by partial reduction at the cys14-cys38 disulfide, treatment with trypsin, purification by HPLC and re-oxidation of the cys14-cys38 disulfide
References: UniProt: P00974
#3: Protein/peptide Pancreatic trypsin inhibitor / Basic protease inhibitor / BPTI / BPI / Aprotinin


Mass: 4820.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P00974

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Non-polymers , 5 types, 369 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 295 K / pH: 8
Details: 0.2M lithium sulfate, 0.1M tris, 34% (w/v) PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Dec 3, 2007 / Details: OSMIC CONFOCAL MAX-FLUX (GREEN)
RadiationMonochromator: OSMIC CONFOCAL MAX-FLUX (GREEN) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.46→30 Å / Num. obs: 51853 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 14.9 % / Biso Wilson estimate: 17.7 Å2 / Rsym value: 0.051 / Net I/σ(I): 22.1
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 6.7 / Rsym value: 0.205 / % possible all: 98.4

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Processing

Software
NameClassification
SBC-Collectdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TGI

3tgi


Resolution: 1.46→30 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: SIMULATED ANNEALING TORSION ANGLE REFINEMENT, POSITIONAL REFINEMENT, RESTRAINED ISOTROPIC INDIVIDUAL B-VALUE REFINEMENT, COUPLED WITH MODEL ADJUSTMENT ON THE BASIS OF SIGMA-A WEIGHTED AND ...Details: SIMULATED ANNEALING TORSION ANGLE REFINEMENT, POSITIONAL REFINEMENT, RESTRAINED ISOTROPIC INDIVIDUAL B-VALUE REFINEMENT, COUPLED WITH MODEL ADJUSTMENT ON THE BASIS OF SIGMA-A WEIGHTED AND COMPOSITE SIMULATED ANNEALING OMIT ELECTRON DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 4131 7.9 %RANDOM, BUT IDENTICAL TO THOSE IDENTIFIED FOR PDB ENTRY 3FP6
Rwork0.175 ---
obs0.175 51811 99.8 %-
all-51811 --
Solvent computationSolvent model: CNS SOLVE / Bsol: 33.26 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 12.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.46→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2245 0 58 371 2674
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0049
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.0851.5
X-RAY DIFFRACTIONc_mcangle_it1.382
X-RAY DIFFRACTIONc_scbond_it1.32
X-RAY DIFFRACTIONc_scangle_it1.872.5
LS refinement shellResolution: 1.46→1.55 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2152 687 8.1 %
Rwork0.2012 7774 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ligand.paramligand.top

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