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- PDB-1ppe: THE REFINED 2.0 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF THE COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 1ppe
TitleTHE REFINED 2.0 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN BOVINE BETA-TRYPSIN AND CMTI-I, A TRYPSIN INHIBITOR FROM SQUASH SEEDS (CUCURBITA MAXIMA): TOPOLOGICAL SIMILARITY OF THE SQUASH SEED INHIBITORS WITH THE CARBOXYPEPTIDASE A INHIBITOR FROM POTATOES
Components
  • TRYPSIN
  • TRYPSIN INHIBITOR CMTI-I
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Plant trypsin inhibitors / Proteinase inhibitor I7, squash / Squash family serine protease inhibitor / Squash family of serine protease inhibitors signature. / Proteinase/amylase inhibitor domain superfamily / 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 domain profile. ...Plant trypsin inhibitors / Proteinase inhibitor I7, squash / Squash family serine protease inhibitor / Squash family of serine protease inhibitors signature. / Proteinase/amylase inhibitor domain superfamily / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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 / Trypsin inhibitor 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBode, W. / Huber, R.
Citation
Journal: FEBS Lett. / Year: 1989
Title: The refined 2.0 A X-ray crystal structure of the complex formed between bovine beta-trypsin and CMTI-I, a trypsin inhibitor from squash seeds (Cucurbita maxima). Topological similarity of the ...Title: The refined 2.0 A X-ray crystal structure of the complex formed between bovine beta-trypsin and CMTI-I, a trypsin inhibitor from squash seeds (Cucurbita maxima). Topological similarity of the squash seed inhibitors with the carboxypeptidase A inhibitor from potatoes
Authors: Bode, W. / Greyling, H.J. / Huber, R. / Otlewski, J. / Wilusz, T.
#1: Journal: Curr.Opin.Struct.Biol. / Year: 1991
Title: Ligand Binding: Proteinase-Protein Inhibitor Interactions
Authors: Bode, W. / Huber, R.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Nuclear Magnetic Resonance Solution and X-Ray Structures of Squash Trypsin Inhibitor Exhibit the Same Conformation of the Proteinase Binding Loop
Authors: Holak, T.A. / Bode, W. / Huber, R. / Otlewski, J. / Wilusz, T.
#3: Journal: Biochem.Biophys.Res.Commun. / Year: 1985
Title: The Squash Family of Serine Proteinase Inhibitors. Amino Acid Sequences and Association Equilibrium Constants of Inhibitors from Squash, Summer Squash, Zucchini, and Cucumber Seeds
Authors: Wieczorek, M. / Otlewski, J. / Cook, J. / Parks, K. / Leluk, J. / Wilimowska-Pelc, A. / Polanowski, A. / Wilusz, T. / Laskowski Junior, M.
#4: Journal: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1983
Title: Amino-Acid Sequence of Two Trypsin Isoinhibitors, Itd I and Itd III from Squash Seeds (Cucurbita Maxima)
Authors: Wilusz, T. / Wieczorek, M. / Polanowski, A. / Denton, A. / Cook, J. / Laskowski Junior, M.
#5: Journal: J.Mol.Biol. / Year: 1975
Title: The Refined Crystal Structure of Bovine Beta-Trypsin at 1.8 Angstroms Resolution. Crystallographic Refinement, Calcium Binding Site, Benzamidine Binding Site and Active Site at Ph 7.0
Authors: Bode, W. / Schwager, P.
History
DepositionOct 24, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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

Downloads & links

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Assembly

Deposited unit
E: TRYPSIN
I: TRYPSIN INHIBITOR CMTI-I


Theoretical massNumber of molelcules
Total (without water)26,6042
Polymers26,6042
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-7 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.280, 55.470, 74.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: GLU E 70 - ASP E 71 OMEGA ANGLE = 149.885 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: SEED / References: UniProt: P00760, trypsin
#2: Protein/peptide TRYPSIN INHIBITOR CMTI-I


Mass: 3279.919 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P01074
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 5 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG60001reservoir
20.1 Mphosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 14191 / % possible obs: 81 % / Num. measured all: 54864 / Rmerge(I) obs: 0.073

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Processing

Software
NameClassification
SQUASHphasing
EREFrefinement
RefinementResolution: 2→6 Å / Rfactor Rwork: 0.151
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 0 140 1991
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.02
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.7
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: EREF / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection obs: 13077 / Rfactor obs: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15 Å2
Refine LS restraints
*PLUS
Type: o_angle_d / Dev ideal: 2.7

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