+Open data
-Basic information
Entry | Database: PDB / ID: 2zk9 | |||||||||
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Title | Crystal Structure of Protein-glutaminase | |||||||||
Components | Protein-glutaminase | |||||||||
Keywords | HYDROLASE / deamidation glutaminase | |||||||||
Function / homology | Protein glutaminase / Glutaminase / C8orf32 fold - #30 / C8orf32 fold / Roll / Alpha Beta / Protein-glutaminase Function and homology information | |||||||||
Biological species | Chryseobacterium proteolyticum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.15 Å | |||||||||
Authors | Hashizume, R. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal structures of protein glutaminase and its pro forms converted into enzyme-substrate complex Authors: Hashizume, R. / Maki, Y. / Mizutani, K. / Takahashi, N. / Matsubara, H. / Sugita, A. / Sato, K. / Yamaguchi, S. / Mikami, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zk9.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zk9.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 2zk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zk9_validation.pdf.gz | 435.1 KB | Display | wwPDB validaton report |
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Full document | 2zk9_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 2zk9_validation.xml.gz | 15 KB | Display | |
Data in CIF | 2zk9_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/2zk9 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/2zk9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19876.283 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chryseobacterium proteolyticum (bacteria) Strain: 9670 / Plasmid: pN7-9 / Production host: Escherichia coli (E. coli) References: UniProt: Q9AQQ8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Sequence details | RESIDUE 21 GLU (UNP RESIDUE 156 GLN) IS SEEM TO BE DEAMIDATED BY THE ENZYME ITSELF. SELF- ...RESIDUE 21 GLU (UNP RESIDUE 156 GLN) IS SEEM TO BE DEAMIDATED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M sodium citrate, 1M Ammonium Phosphate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 9, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→50 Å / Num. all: 76489 / Num. obs: 76207 / Biso Wilson estimate: 12.68 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.15→10 Å / Num. parameters: 19019 / Num. restraintsaints: 26255 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 101 / Occupancy sum hydrogen: 1277.97 / Occupancy sum non hydrogen: 1839.46 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→10 Å
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Refine LS restraints |
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