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- PDB-1tgt: ON THE DISORDERED ACTIVATION DOMAIN IN TRYPSINOGEN. CHEMICAL LABE... -

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Entry
Database: PDB / ID: 1tgt
TitleON THE DISORDERED ACTIVATION DOMAIN IN TRYPSINOGEN. CHEMICAL LABELLING AND LOW-TEMPERATURE CRYSTALLOGRAPHY
ComponentsTRYPSINOGEN
KeywordsHYDROLASE ZYMOGEN (SERINE PROTEINASE)
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / 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 ...: / 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
METHANOL / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsWalter, J. / Steigemann, W. / Singh, T.P. / Bartunik, H. / Bode, W. / Huber, R.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1982
Title: On the Disordered Activation Domain in Trypsinogen. Chemical Labelling and Low-Temperature Crystallography
Authors: Walter, J. / Steigemann, W. / Singh, T.P. / Bartunik, H. / Bode, W. / Huber, R.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1983
Title: The Geometry of the Reactive Site and of the Peptide Groups in Trypsin. Trypsinogen and its Complexes with Inhibitors
Authors: Marquart, M. / Walter, J. / Deisenhofer, J. / Bode, W. / Huber, R.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1980
Title: Low-Temperature Protein Crystallography. Effect on Flexibility, Temperature Factor, Mosaic Spread, Extinction, and Diffuse Scattering in Two Examples. Bovine Trypsinogen and Fc Fragment
Authors: Singh, T.P. / Bode, W. / Huber, R.
#3: Journal: Acc.Chem.Res. / Year: 1978
Title: Structural Basis of the Activation and Action of Trypsin
Authors: Huber, R. / Bode, W.
#4: Journal: FEBS Lett. / Year: 1978
Title: Crystal Structure Analysis and Refinement of Two Variants of Trigonal Trypsinogen
Authors: Bode, W. / Huber, R.
#5: Journal: J.Mol.Biol. / Year: 1977
Title: Crystal Structure of Bovine Trypsinogen at 1.8 Angstroms Resolution. II. Crystallographic Refinement, Refined Crystal Structure and Comparison with Bovine Trypsin
Authors: Fehlhammer, H. / Bode, W. / Huber, R.
#6: Journal: J.Mol.Biol. / Year: 1976
Title: Crystal Structure of Bovine Trypsinogen at 1.8 Angstroms Resolution. I. Data Collection, Application of Patterson Search Techniques and Preliminary Structural Interpretation
Authors: Bode, W. / Fehlhammer, H. / Huber, R.
History
DepositionOct 26, 1981Processing site: BNL
Revision 1.0Mar 4, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRYPSINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1174
Polymers24,0131
Non-polymers1043
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.400, 55.400, 108.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: SEE REMARKS 4 AND 6.

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Components

#1: Protein TRYPSINOGEN


Mass: 24012.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: PANCREAS / References: UniProt: P00760
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE 229 AMINO ACIDS OF TRYPSINOGEN ARE IDENTIFIED BY THE RESIDUE NUMBERS OF THE HOMOLOGOUS CHYMOTRYPSINOGEN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.53 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
31.5 M1dropMgSO4
41.5 M1reservoirMgSO4
2pancreatic trypsin inhibitor1dropat a molar ratio of 4-1

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Data collection

Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 15890 / % possible obs: 72.4 % / Observed criterion σ(I): 2.5 / Num. measured all: 34340 / Rmerge(I) obs: 0.062

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Processing

RefinementResolution: 1.7→6.5 Å / Rfactor Rwork: 0.187
Details: THERE ARE FOUR *FLEXIBLE* SEGMENTS FOR WHICH THERE IS NO SIGNIFICANT ELECTRON DENSITY IN THE MAP. THESE ARE 1. THREE CLOSELY INTERDIGITATING CHAIN SEGMENTS FORMING THE ACTIVATION DOMAIN GLY ...Details: THERE ARE FOUR *FLEXIBLE* SEGMENTS FOR WHICH THERE IS NO SIGNIFICANT ELECTRON DENSITY IN THE MAP. THESE ARE 1. THREE CLOSELY INTERDIGITATING CHAIN SEGMENTS FORMING THE ACTIVATION DOMAIN GLY 142 - PRO 152 GLY 184A - GLY 193 GLY 216 - ASN 223 2. THE N-TERMINUS FROM VAL 10 THROUGH GLY 18 (THIS DATA ENTRY CONTAINS NO COORDINATES FOR VAL 10 THROUGH LYS 15)
Refinement stepCycle: LAST / Resolution: 1.7→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 1 127 1757
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 6.5 Å / Num. reflection obs: 15890 / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 11.6 Å2
Refine LS restraints
*PLUS
Type: o_bond_d / Dev ideal: 0.19
LS refinement shell
*PLUS
Highest resolution: 1.73 Å / Lowest resolution: 6.5 Å

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