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- PDB-3myw: The Bowman-Birk type inhibitor from mung bean in ternary complex ... -

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Basic information

Entry
Database: PDB / ID: 3myw
TitleThe Bowman-Birk type inhibitor from mung bean in ternary complex with porcine trypsin
Components
  • Bowman-Birk type trypsin inhibitor
  • Trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serine proteinase / Bowman-Birk-type inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


trypsin / digestion / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Cysteine Protease (Bromelain) Inhibitor, subunit H / Cysteine Protease (Bromelain) Inhibitor, subunit H / Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site ...Cysteine Protease (Bromelain) Inhibitor, subunit H / Cysteine Protease (Bromelain) Inhibitor, subunit H / Bowman-Birk serine protease inhibitor family / Bowman-Birk serine protease inhibitors family signature. / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / Ribbon / 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
Trypsin / Bowman-Birk type trypsin inhibitor
Similarity search - Component
Biological speciesSus scrofa (pig)
Vigna radiata var. radiata (mung bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEngh, R.A. / Bode, W. / Huber, R. / Lin, G. / Chi, C.
CitationJournal: Eur.J.Biochem. / Year: 1993
Title: The 0.25-nm X-ray structure of the Bowman-Birk-type inhibitor from mung bean in ternary complex with porcine trypsin.
Authors: Lin, G. / Bode, W. / Huber, R. / Chi, C. / Engh, R.A.
History
DepositionMay 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.name
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / 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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypsin
I: Bowman-Birk type trypsin inhibitor
B: Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9925
Polymers54,9123
Non-polymers802
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-34 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.46, 62.46, 160.01
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Trypsin


Mass: 23463.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00761, trypsin
#2: Protein Bowman-Birk type trypsin inhibitor


Mass: 7985.040 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: P01062
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCES IN THIS ENTRY REFLECT THE BELIEVED SEQUENCES AT THE TIME THE WORK WAS PERFORMED.

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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: 3.28 Å3/Da / Density % sol: 62.52 %
Description: THE AUTHORS ORIGINALLY SOLVED THIS STRUCTURE IN SPACE GROUP P 31 2 1 RELYING ON THE INTERNAL SYMMETRY OF THE INHIBITOR. IN ORDER TO PROCESS THIS ENTRY, THE SPACE GROUP SYMMETRY WAS ...Description: THE AUTHORS ORIGINALLY SOLVED THIS STRUCTURE IN SPACE GROUP P 31 2 1 RELYING ON THE INTERNAL SYMMETRY OF THE INHIBITOR. IN ORDER TO PROCESS THIS ENTRY, THE SPACE GROUP SYMMETRY WAS REDUCED TO P 31 AND THE OCCUPANCIES DOUBLED.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.5M ammonium sulfate, 0.2M sodium potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jul 16, 1990
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→8 Å / Num. all: 13569 / Num. obs: 10516 / % possible obs: 77.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.5→2.61 Å / % possible all: 35

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Processing

Software
NameClassification
MADNESSdata collection
PROTEINmodel building
X-PLORrefinement
PROTEINdata reduction
PROTEINdata scaling
PROTEINphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PDB

3pdb


Resolution: 2.5→8 Å / σ(F): 2 / Stereochemistry target values: XPLOR/CHARMM Param19x /
RfactorNum. reflection
obs0.179 10516
all-13569
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3689 0 2 262 3953

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