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- PDB-1t8l: CRYSTAL STRUCTURE OF THE P1 MET BPTI MUTANT- BOVINE CHYMOTRYPSIN ... -

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Basic information

Entry
Database: PDB / ID: 1t8l
TitleCRYSTAL STRUCTURE OF THE P1 MET BPTI MUTANT- BOVINE CHYMOTRYPSIN COMPLEX
Components
  • Chymotrypsin A
  • Pancreatic trypsin inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CHYMOTRYPSIN / SERINE PROTEINASE / BOVINE PANCREATIC TRYPSIN INHIBITOR / BPTI / PROTEIN-PROTEIN INTERACTION / NON-COGNATE BINDING / S1 POCKET / PRIMARY SPECIFICITY / CRYSTAL STRUCTURE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


chymotrypsin / 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 / serpin family protein binding ...chymotrypsin / 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 / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
Chymotrypsinogen A / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCzapinska, H. / Helland, R. / Otlewski, J. / Smalas, A.O.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structures of five bovine chymotrypsin complexes with P1 BPTI variants.
Authors: Czapinska, H. / Helland, R. / Smalas, A.O. / Otlewski, J.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: STRUCTURAL CONSEQUENCES OF ACCOMMODATION OF FOUR NON-COGNATE AMINO-ACID RESIDUES IN THE S1 POCKET OF BOVINE TRYPSIN AND CHYMOTRYPSIN
Authors: Helland, R. / Czapinska, H. / Leiros, I. / Olufsen, M. / Otlewski, J. / Smalaas, A.O.
#2: Journal: Protein Sci. / Year: 1997
Title: Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): ...Title: Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities
Authors: Scheidig, A.J. / Hynes, T.R. / Pelletier, L.A. / Wells, J.A. / Kossiakoff, A.A.
#3: Journal: J.Mol.Recog. / Year: 1997
Title: Crystal structure of the bovine alpha-chymotrypsin:Kunitz inhibitor complex. An example of multiple protein:protein recognition sites.
Authors: Capasso, C. / Rizzi, M. / Menegatti, E. / Ascenzi, P. / Bolognesi, M.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: ULTRAHIGH-RESOLUTION STRUCTURE OF A BPTI MUTANT
Authors: Addlagatta, A. / Czapinska, H. / Krzywda, S. / Otlewski, J. / Jaskolski, M.
#5: Journal: Acta Crystallogr.,Sect.B / Year: 1975
Title: CRYSTALLOGRAPHIC REFINEMENT OF THE STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR AT 1.5 A RESOLUTION
Authors: Deisenhofer, J. / Steigemann, W.
#6: Journal: Nature / Year: 1967
Title: Three-dimensional structure of tosyl-alpha-chymotrypsin
Authors: Matthews, B.W. / Sigler, P.B. / Henderson, R. / Blow, D.M.
History
DepositionMay 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 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: Chymotrypsin A
B: Pancreatic trypsin inhibitor
C: Chymotrypsin A
D: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,61814
Polymers64,6584
Non-polymers96110
Water9,818545
1
A: Chymotrypsin A
B: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0019
Polymers32,3292
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-72 kcal/mol
Surface area13180 Å2
MethodPISA
2
C: Chymotrypsin A
D: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6175
Polymers32,3292
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-71 kcal/mol
Surface area13230 Å2
MethodPISA
3
A: Chymotrypsin A
B: Pancreatic trypsin inhibitor
hetero molecules

C: Chymotrypsin A
D: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,61814
Polymers64,6584
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Buried area7240 Å2
ΔGint-187 kcal/mol
Surface area23550 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-151 kcal/mol
Surface area24040 Å2
MethodPISA
5
B: Pancreatic trypsin inhibitor
hetero molecules

C: Chymotrypsin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9058
Polymers32,3292
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Buried area1840 Å2
ΔGint-76 kcal/mol
Surface area13560 Å2
MethodPISA
6
A: Chymotrypsin A
hetero molecules

D: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7136
Polymers32,3292
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Buried area1840 Å2
ΔGint-75 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.520, 99.520, 205.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Chymotrypsin A


Mass: 25686.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein Pancreatic trypsin inhibitor / Basic protease inhibitor / BPI / BPTI / Aprotinin


Mass: 6642.742 Da / Num. of mol.: 2 / Mutation: K50M, M87L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PAED4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P00974
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 4.6 Å3/Da / Density % sol: 73.2 %
Description: The author notes that the R merge value noted here is a multiplicity weighted R meas
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50% AMMONIUM SULFATE, 0.1M TRIS, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9312 / Wavelength: 0.9312 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9312 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. all: 98049 / Num. obs: 98034 / % possible obs: 85.3 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.069 / Net I/σ(I): 5.4
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.2 / Num. unique all: 13743 / Rsym value: 0.221 / % possible all: 81.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P2N

1p2n


Resolution: 1.75→14.94 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2961 3 %RANDOM
Rwork0.18 ---
all0.181 97953 --
obs0.181 97953 84.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.4491 Å2 / ksol: 0.415482 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å22.08 Å20 Å2
2--3.25 Å20 Å2
3----6.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-15 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.75→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4524 0 50 545 5119
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.572
X-RAY DIFFRACTIONc_scbond_it1.572
X-RAY DIFFRACTIONc_scangle_it2.252.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.242 473 3 %
Rwork0.223 15199 -
obs-15199 81.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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