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- PDB-1ton: RAT SUBMAXILLARY GLAND SERINE PROTEASE, TONIN. STRUCTURE SOLUTION... -

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Basic information

Entry
Database: PDB / ID: 1ton
TitleRAT SUBMAXILLARY GLAND SERINE PROTEASE, TONIN. STRUCTURE SOLUTION AND REFINEMENT AT 1.8 ANGSTROMS RESOLUTION
ComponentsTONIN
KeywordsHYDROLASE(SERINE PROTEINASE)
Function / homology
Function and homology information


tissue kallikrein / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Activation of Matrix Metalloproteinases / regulation of systemic arterial blood pressure / zymogen activation / serine-type peptidase activity / secretory granule / serine-type endopeptidase activity / extracellular space / metal ion binding
Similarity search - Function
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 ...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
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsFujinaga, M. / James, M.N.G.
Citation
Journal: J.Mol.Biol. / Year: 1987
Title: Rat submaxillary gland serine protease, tonin. Structure solution and refinement at 1.8 A resolution.
Authors: Fujinaga, M. / James, M.N.
#1: Journal: Biochemistry / Year: 1985
Title: Kallikrein-Related M/Rnas of the Rat Submaxillary Gland. Nucleotide Sequences of Four Distinct Types Including Tonin
Authors: Ashley, P.L. / Macdonald, R.J.
#2: Journal: Nature / Year: 1984
Title: Amino Acid Sequence of Rat Submaxillary Tonin Reveals Similarities to Serine Proteases
Authors: Lazure, C. / Leduc, R. / Seidah, N.G. / Thibault, G. / Genest, J. / Chretien, M.
#3: Journal: J.Mol.Biol. / Year: 1978
Title: Crystal Data for Tonin, an Enzyme Involved in the Formation of Angiotensin II
Authors: Hayakawa, K. / Kelly, J.A. / James, M.N.G.
History
DepositionJun 3, 1987Processing site: BNL
Revision 1.0Jan 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX THE SECONDARY STRUCTURE SPECIFICATIONS PRESENTED ON THE *HELIX* AND *TURN* RECORDS BELOW WERE ...HELIX THE SECONDARY STRUCTURE SPECIFICATIONS PRESENTED ON THE *HELIX* AND *TURN* RECORDS BELOW WERE EXTRACTED FROM THE PUBLICATION CITED ON THE *JRNL* RECORDS ABOVE. THIS INFORMATION WAS GENERATED USING THE PROCEDURE DEFINED BY W. KABSCH AND C. SANDER (BIOPOLYMERS, V. 22, P. 2577, 1983).
Remark 700SHEET SHEETS *S1A* AND *S1B* FORM A SANDWICH. SHEETS *S2A* AND *S2B* FORM A SANDWICH.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TONIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7522
Polymers25,6861
Non-polymers651
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TONIN
hetero molecules

A: TONIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5044
Polymers51,3732
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area1700 Å2
ΔGint-86 kcal/mol
Surface area19320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.580, 48.580, 200.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: RESIDUE 219 IS A CIS PROLINE. / 2: SEE REMARK 4.

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Components

#1: Protein TONIN


Mass: 25686.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P00759
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE ZINC ION IS ALSO BONDED TO OE2 GLU 148 OF A SYMMETRY-RELATED MOLECULE.

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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: 46.47 %
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 MPIPES1reservoir
25 mM1reservoirZnSO4
32.1 M1reservoir(NH4)2SO4

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Data collection

Reflection
*PLUS
Biso Wilson estimate: 16.1 Å2
Reflection shell
*PLUS

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→8 Å / Rfactor obs: 0.196 / σ(I): 0
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 1 149 1884
Refinement
*PLUS
σ(I): 1 / Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 14997 / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.013
X-RAY DIFFRACTIONp_angle_d0.0310.018
X-RAY DIFFRACTIONp_planar_d0.0270.018
X-RAY DIFFRACTIONp_plane_restr0.0180.015
X-RAY DIFFRACTIONp_chiral_restr0.1390.08

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