[English] 日本語
Yorodumi
- PDB-1thm: CRYSTAL STRUCTURE OF THERMITASE AT 1.4 ANGSTROMS RESOLUTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1thm
TitleCRYSTAL STRUCTURE OF THERMITASE AT 1.4 ANGSTROMS RESOLUTION
ComponentsTHERMITASE
KeywordsHYDROLASE(SERINE PROTEASE)
Function / homology
Function and homology information


thermitase / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Thermitase-like, domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related ...Thermitase-like, domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.37 Å
AuthorsTeplyakov, A.V. / Kuranova, I.P. / Harutyunyan, E.H.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Crystal structure of thermitase at 1.4 A resolution.
Authors: Teplyakov, A.V. / Kuranova, I.P. / Harutyunyan, E.H. / Vainshtein, B.K. / Frommel, C. / Hohne, W.E. / Wilson, K.S.
#1: Journal: Proteins / Year: 1992
Title: Effects of Eglin-C Binding to Thermitase: Three-Dimensional Structure Comparison of Native Thermitase and Thermitase Eglin-C Complexes
Authors: Gros, P. / Teplyakov, A.V. / Hol, W.G.J.
#2: Journal: Protein Eng. / Year: 1990
Title: Thermitase and Proteinase K: A Comparison of the Refined Three-Dimensional Structures of the Native Enzymes
Authors: Betzel, C. / Teplyakov, A.V. / Harutyunyan, E.H. / Saenger, W. / Wilson, K.S.
#3: Journal: FEBS Lett. / Year: 1989
Title: Crystal Structure of Thermitase from Thermoactinomyces Vulgaris at 2.2 Angstroms Resolution
Authors: Teplyakov, A.V. / Kuranova, I.P. / Harutyunyan, E.H. / Froemmel, C. / Hoehne, W.E.
#4: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1987
Title: X-Ray Structural Investigation of Thermitase at a Resolution of 2.5 Angstroms
Authors: Teplyakov, A.V. / Strokopytov, B.V. / Kuranova, I.P. / Popov, A.N. / Arutyunyan, E.G. / Vainshtein, B.K. / Froemmel, K. / Khene, V.
#5: Journal: Biochim.Biophys.Acta / Year: 1981
Title: Influence of Calcium Binding on the Thermal Stability of Thermitase, a Serine Protease from Thermoactinomyces Vulgaris
Authors: Froemmel, C. / Hoehne, W.E.
History
DepositionFeb 24, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THERMITASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7647
Polymers28,3731
Non-polymers3916
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.950, 64.050, 47.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE PRO 172 IS A CIS PROLINE.
2: PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION PRO 214 - THR 215 OMEGA ANGLE = 358.763

-
Components

#1: Protein THERMITASE


Mass: 28372.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / References: UniProt: P04072, thermitase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: THET_THEVU THERMITASE SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE VAL 199 TRP 199 TRP 208 SER 208 THE AMINO ACID SEQUENCE USED IN THIS ENTRY CONTAINS THESE TWO CORRECTIONS OF THE PUBLISHED CHEMICAL SEQUENCE (MELOUN ET AL., FEBS LETT.,1985, 183, 195-200) WHICH WERE INTRODUCED ON THE BASIS OF THE ELECTRON DENSITY.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.14 %
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 %(w/v)protein1drop
20.1 Msodium acetate1reservoir
32-4 %(v/v)MPD1reservoir
420-25 %(w/v)ammonium sulphate1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 1.4 Å / Num. obs: 43794 / % possible obs: 98.1 % / Rmerge(I) obs: 0.126

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.37→7 Å / σ(F): 0 /
RfactorNum. reflection
obs0.166 45660
Refinement stepCycle: LAST / Resolution: 1.37→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 18 193 2214
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0250.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.983
X-RAY DIFFRACTIONp_mcangle_it2.434.5
X-RAY DIFFRACTIONp_scbond_it4.023
X-RAY DIFFRACTIONp_scangle_it5.194.5
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1420.15
X-RAY DIFFRACTIONp_singtor_nbd0.1570.25
X-RAY DIFFRACTIONp_multtor_nbd0.1490.25
X-RAY DIFFRACTIONp_xhyhbond_nbd0.10.25
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.14
X-RAY DIFFRACTIONp_staggered_tor13.415
X-RAY DIFFRACTIONp_orthonormal_tor26.620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.37 Å / Lowest resolution: 7 Å / Num. reflection all: 45660 / σ(F): 0 / Rfactor all: 0.166
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