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- PDB-1mct: THE REFINED 1.6 ANGSTROMS RESOLUTION CRYSTAL STRUCTURE OF THE COM... -

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Basic information

Entry
Database: PDB / ID: 1mct
TitleTHE REFINED 1.6 ANGSTROMS RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN PORCINE BETA-TRYPSIN AND MCTI-A, A TRYPSIN INHIBITOR OF SQUASH FAMILY
Components
  • BETA-TRYPSIN
  • TRYPSIN INHIBITOR A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / PROTEINASE
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
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
Trypsin / Trypsin inhibitor A
Similarity search - Component
Biological speciesSus scrofa (pig)
Momordica charantia (bitter melon)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsHuang, Q. / Liu, S. / Tang, Y.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Refined 1.6 A resolution crystal structure of the complex formed between porcine beta-trypsin and MCTI-A, a trypsin inhibitor of the squash family. Detailed comparison with bovine beta-trypsin and its complex.
Authors: Huang, Q. / Liu, S. / Tang, Y.
#1: Journal: FEBS Lett. / Year: 1992
Title: Amino Acid Sequencing of a Trypsin Inhibitor by Refined 1.6 Angstroms X-Ray Crystal Structure of its Complex with Porcine Beta-Trypsin
Authors: Huang, Q. / Liu, S. / Tang, Y. / Zeng, F. / Qian, R.
History
DepositionOct 24, 1992Processing 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
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_sheet.number_strands / _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: BETA-TRYPSIN
I: TRYPSIN INHIBITOR A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6953
Polymers26,6552
Non-polymers401
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-20 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.650, 62.650, 124.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein BETA-TRYPSIN


Mass: 23491.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: SEED / References: UniProt: P00761, trypsin
#2: Protein/peptide TRYPSIN INHIBITOR A


Mass: 3163.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Momordica charantia (bitter melon) / Organ: SEED / References: UniProt: P30709
#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.: 135 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: TRYP_PIG SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ASP 145 ASN A 145 GLU 167 GLN A 167 SWISS-PROT ENTRY NAME: ITR2_MOMCH SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE LYS 11 THR I 11 GLN 19 LYS I 19 ASP 24 ALA I 24 THE SEQUENCE USED IN THIS ENTRY WAS DETERMINED BY X-RAY CRYSTALLOGRAPHY. THERE ARE SEVERAL UNCERTAIN ASSIGNMENTS WHICH DIFFER FROM THE CHEMICALLY DETERMINED SEQUENCES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 7 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 Msodium phosphate1drop
235 %sat1dropNaCl
30.2 Msodium phosphate1reservoir
485 %sat1reservoirNaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 32238 / % possible obs: 83 % / Observed criterion σ(I): 2 / Num. measured all: 264792 / Rmerge(I) obs: 0.083

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Processing

Software
NameClassification
SQUASHphasing
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.167 / Rfactor obs: 0.167 / Highest resolution: 1.6 Å
Refinement stepCycle: LAST / Highest resolution: 1.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 1 135 1991
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d14.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 7 Å / Num. reflection obs: 31697 / Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.1

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