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- PDB-5pti: STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR. RESULTS OF JOIN... -

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Basic information

Entry
Database: PDB / ID: 5pti
TitleSTRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR. RESULTS OF JOINT NEUTRON AND X-RAY REFINEMENT OF CRYSTAL FORM II
ComponentsTRYPSIN INHIBITOR
KeywordsHydrolase Inhibitor / PROTEINASE 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 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DEUTERATED WATER / PHOSPHATE ION / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / Resolution: 1 Å
AuthorsWlodawer, A. / Huber, R.
Citation
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.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Pancreatic Trypsin Inhibitor. A New Crystal Form and its Analysis
Authors: Walter, J. / Huber, R.
History
DepositionOct 5, 1984Processing site: BNL
Revision 1.0Oct 29, 1984Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Data collection
Revision 1.4Oct 24, 2018Group: Data collection / Other / Structure summary / Category: pdbx_database_status / struct_keywords
Item: _pdbx_database_status.process_site / _struct_keywords.pdbx_keywords / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6233
Polymers6,5281
Non-polymers952
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.100, 23.400, 28.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THE ATOMS IN THE SIDE CHAIN OF RESIDUES GLU 7 AND MET 52 WERE FOUND TO OCCUPY TWO MAJOR SITES. THESE ATOMS ARE DENOTED WITH ALTERNATE LOCATION INDICATORS *A* AND *B*.
2: HETATM UNK 324 IS PROBABLY A POTASSIUM ION IN A PARTIALLY OCCUPIED SITE.

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Components

#1: Protein 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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: D2O
Nonpolymer detailsHETATM UNX 324 IS PROBABLY A POTASSIUM ION IN A PARTIALLY OCCUPIED SITE.

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.87 %
Crystal grow
*PLUS
pH: 10 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
20.1 MK-Na phosphate1drop

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Data collection

Reflection
*PLUS
Highest resolution: 0.94 Å / Lowest resolution: 9999 Å / Num. all: 33612 / Num. obs: 26499 / % possible obs: 76.4 % / Num. measured all: 41385 / Rmerge(I) obs: 0.049

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Processing

RefinementHighest resolution: 1 Å
Refinement stepCycle: LAST / Highest resolution: 1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms454 0 6 63 523
Refinement
*PLUS
Highest resolution: 1 Å / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_bond_d / Dev ideal: 0.02

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