+Open data
-Basic information
Entry | Database: PDB / ID: 1thm | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THERMITASE AT 1.4 ANGSTROMS RESOLUTION | ||||||
Components | THERMITASE | ||||||
Keywords | HYDROLASE(SERINE PROTEASE) | ||||||
Function / homology | Function and homology information thermitase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Thermoactinomyces vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.37 Å | ||||||
Authors | Teplyakov, 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1thm.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1thm.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 1thm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1thm_validation.pdf.gz | 368 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1thm_full_validation.pdf.gz | 369.5 KB | Display | |
Data in XML | 1thm_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1thm_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/1thm ftp://data.pdbj.org/pub/pdb/validation_reports/th/1thm | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: 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 | 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 | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.14 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 1.4 Å / Num. obs: 43794 / % possible obs: 98.1 % / Rmerge(I) obs: 0.126 |
---|
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.37→7 Å / σ(F): 0 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |