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- PDB-2hex: DECAMERS OBSERVED IN THE CRYSTALS OF BOVINE PANCREATIC TRYPSIN IN... -

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Basic information

Entry
Database: PDB / ID: 2hex
TitleDECAMERS OBSERVED IN THE CRYSTALS OF BOVINE PANCREATIC TRYPSIN INHIBITOR
ComponentsPROTEIN (PANCREATIC TRYPSIN INHIBITOR)
KeywordsBLOOD CLOTTING / BOVINE PANCREATIC TRYPSIN INHIBITOR / PENTAMERIC MOLECULE
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLubkowski, J. / Wlodawer, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Decamers observed in the crystals of bovine pancreatic trypsin inhibitor.
Authors: Lubkowski, J. / Wlodawer, A.
History
DepositionAug 1, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
B: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
C: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
D: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
E: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,40613
Polymers32,6385
Non-polymers7698
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
B: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
C: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
D: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
E: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
hetero molecules

A: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
B: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
C: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
D: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
E: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,81326
Polymers65,27610
Non-polymers1,53716
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area19170 Å2
ΔGint-343 kcal/mol
Surface area22970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.995, 94.995, 158.103
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11C-113-

SO4

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Components

#1: Protein
PROTEIN (PANCREATIC TRYPSIN INHIBITOR)


Mass: 6527.568 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00974
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: USING SOLUTION #32 IN CRYSTAL SCREEN I (HAMPTON RESEARCH), pH 6.5, VAPOR DIFFUSION, HANGING DROP
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
32.0 Mammonium sulfate1reservoir
2HEPES1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1997 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 25235 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.82 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 23
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.47 / % possible all: 99
Reflection
*PLUS
Num. measured all: 333309 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
SHELXL-97refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BPI

1bpi


Resolution: 2.1→10 Å / Num. parameters: 9897 / Num. restraintsaints: 9448 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56 B23 (A**2) : ESTIMATED OVERALL COORDINATE ERROR.
RfactorNum. reflection% reflectionSelection details
Rfree0.2883 2432 11.2 %RANDOM
all0.205 21757 --
obs0.2073 -86.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2446.5
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 40 181 2445
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.025
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.036
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.082
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 11.2 % / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.025

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