[English] 日本語
Yorodumi
- PDB-1tgc: ON THE DISORDERED ACTIVATION DOMAIN IN TRYPSINOGEN. CHEMICAL LABE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tgc
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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.8 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 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRYPSINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0532
Polymers24,0131
Non-polymers401
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.110, 55.110, 109.380
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.

-
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.: 93 / 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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.38 %
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

-
Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 12067 / % possible obs: 65.2 % / Biso Wilson estimate: 16.1 Å2

-
Processing

RefinementHighest resolution: 1.8 Å
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 / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 1 93 1723
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 6.5 Å / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more