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- PDB-3tgk: TRYPSINOGEN MUTANT D194N AND DELETION OF ILE 16-VAL 17 COMPLEXED ... -

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Basic information

Entry
Database: PDB / ID: 3tgk
TitleTRYPSINOGEN MUTANT D194N AND DELETION OF ILE 16-VAL 17 COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI)
Components
  • PANCREATIC TRYPSIN INHIBITOR
  • TRYPSIN II, ANIONIC
KeywordsHYDROLASE/ HYDROLASE INHIBITOR / SERINE PROTEASE / COMPLEX (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 / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / Neutrophil degranulation ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / 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 / 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 / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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 / OTHER / Resolution: 1.7 Å
AuthorsPasternak, A. / White, A. / Jeffery, C.J. / Medina, N. / Cahoon, M. / Ringe, D. / Hedstrom, L.
CitationJournal: 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.
History
DepositionJul 19, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 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
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,4006
Polymers32,0722
Non-polymers3284
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-63 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.580, 92.580, 62.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TRYPSIN II, ANIONIC


Mass: 24734.705 Da / Num. of mol.: 1 / Mutation: DEL(I16,V17), D194N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PYT / Genus (production host): Saccharomyces / Production host: Saccharomyces (fungus) / 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) / References: UniProt: P00974
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 48.56 %
Crystal growpH: 8.5 / Details: 0.2 M LISO4, 0.1 M TRIS, pH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
21 mM1dropHCl
310 mM1dropCaCl2
524 %PEG33501reservoir
60.2 M1reservoirLiSO4
70.1 MTris1reservoir
4BPTI1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 32654 / % possible obs: 95.8 % / Redundancy: 5.5 % / Rsym value: 0.057 / Net I/σ(I): 10
Reflection shellResolution: 1.7→1.76 Å / % possible all: 94.2
Reflection
*PLUS
Num. measured all: 181142 / Rmerge(I) obs: 0.057

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.7→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: ALSO TOPH19.PEP USED
RfactorNum. reflection% reflectionSelection details
Rfree0.218 -10 %RANDOM
Rwork0.184 ---
obs0.184 32654 95.8 %-
Displacement parametersBiso mean: 17.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 16 210 2304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.89
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.264 379
Rwork0.262 3326
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2CA.PARAMCA.TOP
X-RAY DIFFRACTION3SO4.PARAMSO4.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOPH
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.89
LS refinement shell
*PLUS
Rfactor Rfree: 0.264 / Rfactor Rwork: 0.262

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