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- PDB-1tgb: CRYSTAL STRUCTURE OF BOVINE TRYPSINOGEN AT 1.8 ANGSTROMS RESOLUTI... -

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Database: PDB / ID: 1tgb
TitleCRYSTAL STRUCTURE OF BOVINE TRYPSINOGEN AT 1.8 ANGSTROMS RESOLUTION. II. CRYSTALLOGRAPHIC REFINEMENT, REFINED CRYSTAL STRUCTURE AND COMPARISON WITH BOVINE TRYPSIN
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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBode, W. / Fehlhammer, H. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 1977
Title: Crystal structure of bovine trypsinogen at 1-8 A resolution. II. Crystallographic refinement, refined crystal structure and comparison with bovine trypsin.
Authors: Fehlhammer, H. / Bode, W. / Huber, R.
#1: 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.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1980
Title: Low-Temperature Protein Crystallography. 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.
History
DepositionMar 7, 1979Processing site: BNL
Revision 1.0Jun 13, 1979Provider: 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 1.4Nov 6, 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: TRYPSINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0532
Polymers24,0131
Non-polymers401
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.100, 55.100, 109.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: THESE ATOMS WERE NOT FOUND IN THE ELECTRON DENSITY MAP. THEIR COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA.
Components on special symmetry positions
IDModelComponents
11A-849-

HOH

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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) / References: UniProt: P00760
#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.: 120 / 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 Å3/Da / Density % sol: 38.37 %
Crystal grow
*PLUS
Method: other / Details: Bode, W., (1976) J. Mol. Biol., 106, 325.

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 15000 / Num. measured all: 45000

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Processing

RefinementHighest resolution: 1.8 Å
Details: THE TEMPERATURE FACTOR FIELD OF THE ATOM AND HETATM RECORDS CONTAINS THE ATOMIC RADIUS WHICH HAS BEEN TENTATIVELY REFINED. THE OCCUPANCY FACTORS (WEIGHTS) HAVE BEEN REFINED ONLY FOR THE SOLVENT ATOMS.
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 1 120 1750
Refinement
*PLUS
σ(I): 2 / Rfactor all: 0.38 / Rfactor obs: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS

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