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- PDB-1bpi: THE STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR AT 125K: DEF... -

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Basic information

Entry
Database: PDB / ID: 1bpi
TitleTHE STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR AT 125K: DEFINITION OF CARBOXYL-TERMINAL RESIDUES GLYCINE-57 AND ALANINE-58
ComponentsBOVINE PANCREATIC TRYPSIN INHIBITOR
KeywordsPROTEINASE INHIBITOR (TRYPSIN)
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / 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 / negative regulation of platelet aggregation / potassium channel inhibitor activity / 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 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
PHOSPHATE ION / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.09 Å
AuthorsParkin, S. / Rupp, B. / Hope, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of bovine pancreatic trypsin inhibitor at 125 K definition of carboxyl-terminal residues Gly57 and Ala58.
Authors: Parkin, S. / Rupp, B. / Hope, H.
History
DepositionFeb 18, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6232
Polymers6,5281
Non-polymers951
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.390, 22.581, 28.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SIDE CHAINS OF RESIDUES GLU 7 AND ARG 53 WERE FOUND TO OCCUPY TWO MAJOR SITES. THESE ARE DENOTED BY THE ALTERNATE SITE INDICATORS *A* AND *B*.

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Components

#1: Protein BOVINE PANCREATIC TRYPSIN INHIBITOR


Mass: 6527.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00974
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsINITIAL MODEL DERIVED FROM THE COORDINATE SET OF PDB ENTRY 5PTI. PRIOR TO REFINEMENT THE MODEL WAS ...INITIAL MODEL DERIVED FROM THE COORDINATE SET OF PDB ENTRY 5PTI. PRIOR TO REFINEMENT THE MODEL WAS MODIFIED AS FOLLOWS: (I) DISORDER WAS REMOVED, MAJOR CONFORMATIONS INCLUDED AT FULL OCCUPANCY. (II) HYDROGEN ATOMS REMOVED. (III) ISOTROPIC THERMAL PARAMETERS HALVED, CONVERTED TO *U* FORMAT AND ROUNDED TO THE NEAREST 0.01 ANGSTROM SQUARED. (IV) AMINO ACID GEOMETRIES RESTRAINED ACCORDING TO ENGH AND HUBER (1991), ACTA CRYST. A47 PP.392-400.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 34 %
Crystal grow
*PLUS
pH: 10 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mg/mlprotein1drop
20.5 MK-Na phosphate1drop
30.5 MK-Na phosphate1reservoir

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: DIFFRACTOMETER / Date: Jun 1, 1984
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection
*PLUS
Num. obs: 20781 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Num. measured all: 28980

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Processing

Software
NameVersionClassification
SIEMENSXDISKdata collection
SHELXL-93model building
SHELXL-93refinement
XFITdata reduction
SIEMENSXDISKdata reduction
SHELXL-93phasing
RefinementResolution: 1.09→10 Å / σ(F): 0
Details: RESIDUES GLU 7 AND ARG 53 WERE MODELED IN TWO CONFORMATIONS. 145.6 WATER MOLECULES OVER 167 SITES WERE MODELED. 123 ARE AT FULL OCCUPANCY, 39 ARE AT HALF OCCUPANCY AND THE REMAINDER HAVE ...Details: RESIDUES GLU 7 AND ARG 53 WERE MODELED IN TWO CONFORMATIONS. 145.6 WATER MOLECULES OVER 167 SITES WERE MODELED. 123 ARE AT FULL OCCUPANCY, 39 ARE AT HALF OCCUPANCY AND THE REMAINDER HAVE OCCUPANCIES DETERMINED BY THE DISORDER AT RESIDUES GLU 7 AND ARG 53. THE PHOSPHATE WAS MODELED IN TWO CONFORMATIONS. RESTRAINED ANISOTROPIC THERMAL PARAMETERS WERE REFINED. THE COORDINATES IN THIS ENTRY ARE THOSE OF THE ISOTROPIC MODEL. R VALUES FOR THE ISOTROPIC AND ANISOTROPIC MODELS WERE 0.187 AND 0.161 FOR ALL DATA. FREE R VALUES FOR BOTH MODELS WERE INSIGNIFICANTLY DIFFERENT. PROTEIN GEOMETRY FOR MAJOR AND MINOR CONFORMATIONS OF GLU 7 AND ASP 53 WAS CHECKED WITH THE PROCHECK PROGRAM (LASKOWSKI, MACARTHUR, MOSS, THORNTON (1993) J. APPL. CRYST. 26, 283 - 291). THE OMEGA TORSION ANGLE OF ARG 1 SHOWS A MARKED DEVIATION FROM PLANARITY. ELECTRON DENSITY MAPS CLEARLY SUPPORT THIS DISTORTION.
RfactorNum. reflection
obs0.187 20740
Refinement stepCycle: LAST / Resolution: 1.09→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms460 0 11 166 637
Refinement
*PLUS
Rfactor all: 0.187 / Rfactor obs: 0.146 / Rfactor Rfree: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.035
X-RAY DIFFRACTIONs_angle_deg3.1

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