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- PDB-1f5r: RAT TRYPSINOGEN MUTANT COMPLEXED WITH BOVINE PANCREATIC TRYPSIN I... -

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Basic information

Entry
Database: PDB / ID: 1f5r
TitleRAT TRYPSINOGEN MUTANT COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR
Components
  • PANCREATIC TRYPSIN INHIBITOR
  • TRYPSIN II, ANIONIC
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / TRYPSIN PRECURSOR / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsPasternak, A. / White, A. / Cahoon, M. / Ringe, D. / Hedstrom, L.
Citation
Journal: Protein Sci. / Year: 2001
Title: The energetic cost of induced fit catalysis: Crystal structures of trypsinogen mutants with enhanced activity and inhibitor affinity.
Authors: Pasternak, A. / White, A. / Jeffery, C.J. / Medina, N. / Cahoon, M. / Ringe, D. / Hedstrom, L.
#1: Journal: Protein Sci. / Year: 1999
Title: Comparison of Anionic and Cationic Trypsinogens: the Anionic Activation Domain is More Flexible in Solution and Differs in its Mode of BPTI Binding in the Crystal Structure
Authors: Pasternak, A. / Ringe, D. / Hedstrom, L.
#2: Journal: Biochemistry / Year: 1998
Title: Activating a Zymogen Without Proteolytic Processing: Mutation of Lys15 and Asn194 Activates Trypsinogen.
Authors: Pasternak, A. / Liu, X. / Lin, T.-Y. / Hedstrom, L.
History
DepositionJun 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN II, ANIONIC
I: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1143
Polymers32,0742
Non-polymers401
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-20 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.568, 92.568, 62.126
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TRYPSIN II, ANIONIC


Mass: 24736.742 Da / Num. of mol.: 1 / Mutation: DELTA-I16-V17, Q156K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PYT / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00763, trypsin
#2: Protein PANCREATIC TRYPSIN INHIBITOR / BPTI


Mass: 7337.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: PANCREAS / 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.: 270 / 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: 48.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG 3380, 300 mM Ammonium acetate, 100 mM Sodium acetate, , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
21 mM1dropHCl
310 mM1dropCaCl2
522 %PEG33801reservoir
60.3 Mammonium acetate1reservoir
70.1 Msodium citrate1reservoir
4BPTI1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→21.69 Å / Num. all: 35860 / Num. obs: 195481 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.45 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.56
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 1.92 % / Rmerge(I) obs: 0.242 / Num. unique all: 1494 / % possible all: 80.9
Reflection
*PLUS
Num. obs: 35860 / Num. measured all: 195481 / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 1.65→21.69 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3489 10 %RANDOM
Rwork0.189 ---
all-31408 --
obs-34897 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.0572 Å2 / ksol: 0.340608 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0.93 Å20 Å2
2--0.26 Å20 Å2
3----0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.65→21.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 1 270 2372
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it0.581.5
X-RAY DIFFRACTIONc_mcangle_it1.042
X-RAY DIFFRACTIONc_scbond_it0.722
X-RAY DIFFRACTIONc_scangle_it1.152.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 505 10.4 %
Rwork0.313 4328 -
obs--78.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.189 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.315 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.313

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