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- PDB-1ejm: CRYSTAL STRUCTURE OF THE BPTI ALA16LEU MUTANT IN COMPLEX WITH BOV... -

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Basic information

Entry
Database: PDB / ID: 1ejm
TitleCRYSTAL STRUCTURE OF THE BPTI ALA16LEU MUTANT IN COMPLEX WITH BOVINE TRYPSIN
Components
  • BETA-TRYPSIN
  • PANCREATIC TRYPSIN INHIBITOR
KeywordsHYDROLASE/INHIBITOR / Complex / HYDROLASE-INHIBITOR COMPLEX
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 / trypsin / serpin family protein binding ...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 / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / metal ion binding
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 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
Serine protease 1 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsOtlewski, J. / Smalas, A. / Helland, R. / Grzesiak, A. / Krowarsch, D.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Substitutions at the P(1) position in BPTI strongly affect the association energy with serine proteinases.
Authors: Grzesiak, A. / Helland, R. / Smalas, A.O. / Krowarsch, D. / Dadlez, M. / Otlewski, J.
History
DepositionMar 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.6Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-TRYPSIN
B: PANCREATIC TRYPSIN INHIBITOR
C: BETA-TRYPSIN
D: PANCREATIC TRYPSIN INHIBITOR
E: BETA-TRYPSIN
F: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,86418
Polymers89,7126
Non-polymers1,15312
Water11,007611
1
A: BETA-TRYPSIN
B: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2886
Polymers29,9042
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: BETA-TRYPSIN
D: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3847
Polymers29,9042
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: BETA-TRYPSIN
F: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1925
Polymers29,9042
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.870, 180.870, 170.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsThere are 3 complex molecules in the asymmetric unit.

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Components

#1: Protein BETA-TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: PURCHASED FROM SIGMA / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin
#2: Protein PANCREATIC TRYPSIN INHIBITOR / BASIC PROTEASE INHIBITOR / BPI / APROTININ


Mass: 6579.624 Da / Num. of mol.: 3 / Mutation: K15R, A16L, M52L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00974
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 3.88 Å3/Da / Density % sol: 68.34 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 48% saturated ammonium sulphate, 0.1 M Hepes buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 37K
Crystal grow
*PLUS
Details: Helland, R., (1999) J. Mol. Biol., 287, 923.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127 mg/mlprotein1drop
248-50 %satammonium sulfate1reservoir
30.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.93
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.85→15 Å / Num. all: 1193911 / Num. obs: 119391 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 5.4
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.412 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 1360301

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Processing

Software
NameVersionClassification
MAR345data collection
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 1.85→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Eng & Huber
RfactorNum. reflectionSelection details
Rfree0.233 8167 Random
Rwork0.211 --
all0.212 119391 -
obs0.212 99523 -
Refinement stepCycle: LAST / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6264 0 60 611 6935
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_d1.3
X-RAY DIFFRACTIONx_torsion_deg24.8
X-RAY DIFFRACTIONx_torsion_impr_deg0.72
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d24.8

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