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- PDB-1f2s: CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN BOVINE BETA-TRYPS... -

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Basic information

Entry
Database: PDB / ID: 1f2s
TitleCRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN BOVINE BETA-TRYPSIN AND MCTI-A, A TRYPSIN INHIBITOR OF SQUASH FAMILY AT 1.8 A RESOLUTION
Components
  • TRYPSIN
  • TRYPSIN INHIBITOR A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEINASE-INHIBITOR COMPLEX / TRYPSIN / 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
Proteinase inhibitor I7, squash / Squash family serine protease inhibitor / Squash family of serine protease inhibitors signature. / Plant trypsin inhibitors / Proteinase/amylase inhibitor domain superfamily / : / 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 ...Proteinase inhibitor I7, squash / Squash family serine protease inhibitor / Squash family of serine protease inhibitors signature. / Plant trypsin inhibitors / Proteinase/amylase inhibitor domain superfamily / : / 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 / Trypsin inhibitor 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Momordica charantia (bitter melon)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsZhu, Y. / Huang, Q. / Qian, M. / Jia, Y. / Tang, Y.
Citation
Journal: J.Protein Chem. / Year: 1999
Title: Crystal structure of the complex formed between bovine beta-trypsin and MCTI-A, a trypsin inhibitor of squash family, at 1.8-A resolution.
Authors: Zhu, Y. / Huang, Q. / Qian, M. / Jia, Y. / Tang, Y.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: REFINED 1.6A RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN PORCINE BETA-TRYPSIN AND MCTI-A, A TRYPSIN INHIBITOR OF THE SQUASH FAMILY
Authors: Huang, Q. / Liu, S. / Tang, Y.
#2: Journal: FEBS Lett. / Year: 1992
Title: AMINO ACID SEQUENCING OF A TRYPSIN INHIBITOR BY REFINED 1.6A X-RAY CRYSTAL STRUCTURE OF ITS COMPLEX WITH PORCINE BETA-TRYPSIN
Authors: Huang, Q. / Liu, S. / Tang, Y. / Zeng, F. / Qian, R.
History
DepositionMay 29, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionMay 31, 2000ID: 1MCU
Revision 1.0Jun 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: TRYPSIN
I: TRYPSIN INHIBITOR A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6163
Polymers26,5762
Non-polymers401
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-20 kcal/mol
Surface area10140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.76, 55.55, 74.47
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PANCREATIC / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREATIC / References: UniProt: P00760, trypsin
#2: Protein/peptide TRYPSIN INHIBITOR A


Mass: 3251.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SEED / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: P10295
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: PEG6000, soduim phosphate buffer, pH 5.10, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5
Details: drop consists of equal volume of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112.8 mg/mlbeta-trypsin1drop
22.2 mg/mlMCTI-A1drop
311 mMTris-HCl1drop
410 mM1dropHAc
50.1 Msodium phosphate1reservoirprecipitant
620 %PEG60001reservoirprecipitant

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 26, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.79→75 Å / Num. all: 23032 / Num. obs: 20741 / % possible obs: 86.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.7
Reflection shellResolution: 1.79→1.86 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.213 / Num. unique all: 1607 / % possible all: 63.4
Reflection shell
*PLUS
% possible obs: 63.4 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PPE

1ppe


Resolution: 1.79→7 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1995 -RANDOM
Rwork0.177 ---
all0.181 20277 --
obs0.181 20277 86.2 %-
Refinement stepCycle: LAST / Resolution: 1.79→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 1 207 2055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.41
X-RAY DIFFRACTIONx_torsion_deg26.2
X-RAY DIFFRACTIONx_torsion_impr_deg1.16
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION3PARDNA.PROTOPDNA.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.16

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