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Yorodumi- PDB-1mki: Crystal Structure of Bacillus Subtilis Probable Glutaminase, APC1040 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mki | ||||||
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Title | Crystal Structure of Bacillus Subtilis Probable Glutaminase, APC1040 | ||||||
Components | Probable Glutaminase ybgJ | ||||||
Keywords | HYDROLASE / Structural Genomics / Probable glutaminase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information glutamine catabolic process / glutamate biosynthetic process / glutaminase / glutaminase activity Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Kim, Y. / Dementieva, I. / Vinokour, E. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Functional and structural characterization of four glutaminases from Escherichia coli and Bacillus subtilis. Authors: Brown, G. / Singer, A. / Proudfoot, M. / Skarina, T. / Kim, Y. / Chang, C. / Dementieva, I. / Kuznetsova, E. / Gonzalez, C.F. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mki.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mki.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mki_validation.pdf.gz | 470.7 KB | Display | wwPDB validaton report |
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Full document | 1mki_full_validation.pdf.gz | 490.1 KB | Display | |
Data in XML | 1mki_validation.xml.gz | 30 KB | Display | |
Data in CIF | 1mki_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/1mki ftp://data.pdbj.org/pub/pdb/validation_reports/mk/1mki | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37139.520 Da / Num. of mol.: 2 / Mutation: N-terminal insertion SNA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YBGJ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31465, glutaminase #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-FMT / | #4: 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: 2.24 Å3/Da / Density % sol: 45.14 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 1500, HEPES, sodium chloride, Glycerol, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / 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: APS / Beamline: 19-ID / Wavelength: 0.97910, 0.97921, 0.954 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Feb 13, 2002 / Details: mirror | ||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. all: 46201 / Num. obs: 46201 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 5.4 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4499 / % possible all: 98.5 | ||||||||||||
Reflection shell | *PLUS % possible obs: 98.5 % / Redundancy: 9.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→40.69 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.6142 Å2 / ksol: 0.369277 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.29 Å / Luzzati sigma a free: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 40.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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