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- PDB-8pti: CRYSTAL STRUCTURE OF A Y35G MUTANT OF BOVINE PANCREATIC TRYPSIN I... -

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Basic information

Entry
Database: PDB / ID: 8pti
TitleCRYSTAL STRUCTURE OF A Y35G MUTANT OF BOVINE PANCREATIC TRYPSIN INHIBITOR
ComponentsBOVINE PANCREATIC TRYPSIN INHIBITOR
KeywordsPROTEINASE INHIBITOR (TRYPSIN)
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space
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
Similarity search - Domain/homology
Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsHousset, D. / Kim, K.-S. / Fuchs, J. / Woodward, C. / Wlodawer, A.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Crystal structure of a Y35G mutant of bovine pancreatic trypsin inhibitor.
Authors: Housset, D. / Kim, K.S. / Fuchs, J. / Woodward, C. / Wlodawer, A.
#1: Journal: Protein Eng. / Year: 1990
Title: Structural Effects Induced by Removal of a Disulfide-Bridge. The X-Ray Structure of the C30A(Slash)C51A Mutant of Basic Pancreatic Trypsin Inhibitor at 1.6 Angstroms
Authors: Eigenbrot, C. / Randal, M. / Kossiakoff, A.A.
#2: Journal: Biochemistry / Year: 1990
Title: X-Ray Crystal Structure of the Protease Inhibitor Domain of Alzheimer'S Amyloid Beta-Protein Precursor
Authors: Hynes, T.R. / Randal, M. / Kennedy, L.A. / Eigenbrot, C. / Kossiakoff, A.A.
#3: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of Form III Crystals of Bovine Pancreatic Trypsin Inhibitor.
Authors: Wlodawer, A. / Nachman, J. / Gilliland, G.L. / Gallagher, W. / Woodward, C.
#4: Journal: J.Mol.Biol. / Year: 1984
Title: Structure of Bovine Pancreatic Trypsin Inhibitor. Results of Joint Neutron and X-Ray Refinement of Crystal Form II
Authors: Wlodawer, A. / Walter, J. / Huber, R. / Sjolin, L.
#5: Journal: J.Mol.Biol. / Year: 1987
Title: Comparison of Two Highly Refined Structures of Bovine Pancreatic Trypsin Inhibitor
Authors: Wlodawer, A. / Deisenhofer, J. / Huber, R.
#6: Journal: J.Mol.Biol. / Year: 1983
Title: Pancreatic Trypsin Inhibitor. A New Crystal Form and its Analysis
Authors: Walter, J. / Huber, R.
History
DepositionDec 17, 1990Processing site: BNL
Revision 1.0Apr 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BOVINE PANCREATIC TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)6,4211
Polymers6,4211
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.750, 46.750, 50.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-205-

HOH

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Components

#1: Protein BOVINE PANCREATIC TRYPSIN INHIBITOR


Mass: 6421.446 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00974
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal grow
*PLUS
pH: 9.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.35 M1dropK2HPO4
22-7 mg/mlprotein1drop
31.5 M1reservoirK2HPO4

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Data collection

Reflection
*PLUS
Highest resolution: 1.78 Å / Num. obs: 5482 / % possible obs: 95.6 % / Observed criterion σ(I): 1.5 / Num. measured all: 47955 / Rmerge(I) obs: 0.071

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.159 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms446 0 0 70 516
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.8 Å / Num. reflection obs: 5402 / σ(F): 2 / Rfactor obs: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_deg0.0330.03
X-RAY DIFFRACTIONp_planar_d0.0480.05
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.2160.15
X-RAY DIFFRACTIONp_mcbond_it2.4773
X-RAY DIFFRACTIONp_scbond_it4.6094
X-RAY DIFFRACTIONp_mcangle_it2.8363.5
X-RAY DIFFRACTIONp_scangle_it6.8795

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