+Open data
-Basic information
Entry | Database: PDB / ID: 1a2z | ||||||
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Title | PYRROLIDONE CARBOXYL PEPTIDASE FROM THERMOCOCCUS LITORALIS | ||||||
Components | PYRROLIDONE CARBOXYL PEPTIDASE | ||||||
Keywords | PEPTIDASE / N-PYROGLUTAMATE HYDROLYSIS | ||||||
Function / homology | Function and homology information pyroglutamyl-peptidase I / pyroglutamyl-peptidase activity / proteolysis / cytosol Similarity search - Function | ||||||
Biological species | Thermococcus litoralis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.73 Å | ||||||
Authors | Singleton, M.R. / Isupov, M.N. / Littlechild, J.A. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: X-ray structure of pyrrolidone carboxyl peptidase from the hyperthermophilic archaeon Thermococcus litoralis. Authors: Singleton, M. / Isupov, M. / Littlechild, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a2z.cif.gz | 190.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a2z.ent.gz | 159.8 KB | Display | PDB format |
PDBx/mmJSON format | 1a2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a2z_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 1a2z_full_validation.pdf.gz | 469.3 KB | Display | |
Data in XML | 1a2z_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 1a2z_validation.cif.gz | 59.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/1a2z ftp://data.pdbj.org/pub/pdb/validation_reports/a2/1a2z | 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 24776.785 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: CYS 143 OXIDIZED IN EACH SUBUNIT / Source: (gene. exp.) Thermococcus litoralis (archaea) / Description: CAMR, PORTON DOWN, WILTSHIRE, UK / Gene: PCP / Plasmid: PKK223-3 / Cellular location (production host): CYTOSOL / Gene (production host): PCP / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / Variant (production host): JS5 / References: UniProt: O07883, pyroglutamyl-peptidase I #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 35% AMMONIUM SULFATE, 50 MM POTASSIUM PHOSPHATE, PH 6.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.9096 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 29, 1997 / Details: SEGMENTED MIRROR |
Radiation | Monochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9096 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.73 Å / Num. obs: 104008 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 3 / Rsym value: 0.284 / % possible all: 97 |
Reflection | *PLUS % possible obs: 97.4 % / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 97 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.73→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.73→20 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.187 / Rfactor Rfree: 0.214 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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