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- PDB-1g9i: CRYSTAL STRUCTURE OF BETA-TRYSIN COMPLEX IN CYCLOHEXANE -

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Basic information

Entry
Database: PDB / ID: 1g9i
TitleCRYSTAL STRUCTURE OF BETA-TRYSIN COMPLEX IN CYCLOHEXANE
Components
  • BOWMAN-BIRK TYPE TRYPSIN INHIBITOR
  • TRYPSINOGEN, CATIONIC
KeywordsHYDROLASE/HYDROLASE INHIBITOR / TRYPSIN-INHIBITOR COMPLEX / ORGANIC MEDIA / 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
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 / 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. ...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 / 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 / Bowman-Birk type trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhu, G. / Huang, Q. / Zhu, Y. / Li, Y. / Chi, C. / Tang, Y.
Citation
Journal: Biochim.Biophys.Acta / Year: 2001
Title: X-Ray study on an artificial mung bean inhibitor complex with bovine beta-trypsin in neat cyclohexane.
Authors: Zhu, G. / Huang, Q. / Zhu, Y. / Li, Y. / Chi, C. / Tang, Y.
#1: Journal: J.Biochem.(Tokyo) / Year: 1994
Title: Studies on an Artificial Trypsin Inhibitor Peptide Derived from the Mung Bean Inhibitor
Authors: Li, Y. / Huang, Q. / Zhang, S. / Liu, S. / Chi, C. / Tang, Y.
History
DepositionNov 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: TRYPSINOGEN, CATIONIC
I: BOWMAN-BIRK TYPE TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9685
Polymers25,7362
Non-polymers2323
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-39 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.38, 63.35, 69.04
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRYPSINOGEN, CATIONIC


Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: BETA-TRYPSIN / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin
#2: Protein/peptide BOWMAN-BIRK TYPE TRYPSIN INHIBITOR / ARTIFICIAL MUNG BEAN INHIBITOR


Mass: 2411.823 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence is based on mimic bean trypsin inhibitor.
References: UniProt: P01062
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 2M ammonium sulphate, 0.2M phosphate buffer, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Temperature: 24 ℃ / Details: Li, Y., (1994) J.Biochem.(Tokyo), 116, 18.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate1drop
20.2 Mphosphate1drop
32 Mammonium sulfate1reservoir
40.2 Mphosphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→70 Å / Num. all: 14471 / Num. obs: 12041 / % possible obs: 83.2 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 0.75 / Redundancy: 3.7 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 2 / % possible all: 62.3
Reflection shell
*PLUS
% possible obs: 62.3 %

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Processing

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

1smf


Resolution: 2.2→7 Å / σ(F): 1.5 / σ(I): 0.75 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.243 1193 RANDOM
Rwork0.185 --
all0.193 11555 -
obs0.193 11555 -
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 11 180 1982
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d1.5
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_improper_angle_d1.37
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.2-2.30.3471160.26X-RAY DIFFRACTION1080
2.3-2.410.2891100.239X-RAY DIFFRACTION1146
2.41-2.560.2861270.228X-RAY DIFFRACTION1326
2.56-2.740.2651590.218X-RAY DIFFRACTION1422
2.74-30.2771550.204X-RAY DIFFRACTION1489
3-3.390.2171720.175X-RAY DIFFRACTION1604
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_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37

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