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- PDB-2ptn: ON THE DISORDERED ACTIVATION DOMAIN IN TRYPSINOGEN. CHEMICAL LABE... -

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Basic information

Entry
Database: PDB / ID: 2ptn
TitleON THE DISORDERED ACTIVATION DOMAIN IN TRYPSINOGEN. CHEMICAL LABELLING AND LOW-TEMPERATURE CRYSTALLOGRAPHY
ComponentsTRYPSIN
KeywordsHYDROLASE (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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.55 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: Miami Winter Symp. / Year: 1976
Title: Structural Studies on the Pancreatic Trypsin Inhibitor-Trypsin Complex and its Free Components. Structure and Function Relationships in Serine Protease Inhibition and Catalysis
Authors: Bode, W. / Schwager, P. / Huber, R.
#3: Journal: J.Mol.Biol. / Year: 1975
Title: The Refined Crystal Structure of Bovine Beta-Trypsin at 1.8 Angstroms Resolution. II. Crystallographic Refinement, Calcium Binding Site, Benzamidine Binding Site and Active Site at Ph 7.0
Authors: Bode, W. / Schwager, P.
#4: Journal: J.Mol.Biol. / Year: 1975
Title: The Refined Crystal Structure of Bovine Beta-Trypsin at 1.8 Angstroms Resolution. I. Crystallization, Data Collection and Application of Patterson Search Techniques
Authors: Fehlhammer, H. / Bode, W.
#5: Journal: FEBS Lett. / Year: 1975
Title: The Single Calcium-Binding Site of Crystalline Bovine Beta-Trypsin
Authors: Bode, W. / Schwager, P.
#6: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionOct 26, 1981Processing site: BNL
SupersessionMar 4, 1982ID: 1PTN
Revision 1.0Mar 4, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3642
Polymers23,3241
Non-polymers401
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.890, 58.520, 67.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SEE REMARK 4.

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Components

#1: Protein TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.16 %
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: 1.55 Å

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Processing

RefinementResolution: 1.55→6.5 Å / Rfactor Rwork: 0.193
Refinement stepCycle: LAST / Resolution: 1.55→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 1 82 1712
Refinement
*PLUS
Num. reflection obs: 23560 / Highest resolution: 1.55 Å / Lowest resolution: 6.5 Å / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.5 Å2
LS refinement shell
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 1.58 Å

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