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Yorodumi- PDB-1hpg: A glutamic acid specific serine protease utilizes a novel histidi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hpg | ||||||
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Title | A glutamic acid specific serine protease utilizes a novel histidine triad in substrate binding | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information glutamyl endopeptidase II / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / extracellular region Similarity search - Function | ||||||
Biological species | Streptomyces griseus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.5 Å | ||||||
Authors | Nienaber, V.L. / Birktoft, J.J. | ||||||
Citation | Journal: Biochemistry / Year: 1993 Title: A glutamic acid specific serine protease utilizes a novel histidine triad in substrate binding. Authors: Nienaber, V.L. / Breddam, K. / Birktoft, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hpg.cif.gz | 45.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hpg.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hpg_validation.pdf.gz | 367.1 KB | Display | wwPDB validaton report |
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Full document | 1hpg_full_validation.pdf.gz | 366.9 KB | Display | |
Data in XML | 1hpg_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 1hpg_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/1hpg ftp://data.pdbj.org/pub/pdb/validation_reports/hp/1hpg | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: SER A 79 - GLY A 80 OMEGA = 320.79 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: CIS PROLINE - PRO A 99 |
-Components
#1: Protein | Mass: 18279.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: sprE References: UniProt: Q54211, UniProt: Q07006*PLUS, glutamyl endopeptidase II |
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#2: Protein/peptide | |
#3: Water | ChemComp-HOH / |
Nonpolymer details | HOH 401 FITS THE CRITERIA OF A SODIUM ATOM BUT WAS REFINED AS AN ORDERED SOLVENT. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.3 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 22913 / % possible obs: 94.4 % / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. all: 13006 / Num. measured all: 90655 / Rmerge(I) obs: 0.083 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.181 / Rfactor obs: 0.181 / Highest resolution: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Rfactor obs: 0.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 3.18 |