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Yorodumi- PDB-2o8r: Crystal Structure of Polyphosphate Kinase from Porphyromonas Ging... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o8r | ||||||
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Title | Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis | ||||||
Components | Polyphosphate kinase | ||||||
Keywords | TRANSFERASE / KINASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / NYSGRC / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information polyphosphate kinase complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / polyphosphate kinase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Porphyromonas gingivalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Sauder, J.M. / Dickey, M. / Adams, J.M. / Ozyurt, S. / Wasserman, S.R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis Authors: Patskovsky, Y. / Toro, R. / Sauder, J.M. / Dickey, M. / Adams, J.M. / Ozyurt, S. / Wasserman, S.R. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o8r.cif.gz | 272.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o8r.ent.gz | 221.5 KB | Display | PDB format |
PDBx/mmJSON format | 2o8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/2o8r ftp://data.pdbj.org/pub/pdb/validation_reports/o8/2o8r | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
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Details | likely homo-dimer, the asymmetric unit contains a homodimer |
-Components
#1: Protein | Mass: 82967.008 Da / Num. of mol.: 2 / Mutation: M1L, A635T, A690T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: ATCC BAA-308 / W83 / Gene: ppk / Plasmid: BC-pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q7MTR1, ATP-polyphosphate phosphotransferase #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: 2.91 Å3/Da / Density % sol: 57.8 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.6M MALIC ACID, PH 7.0, 0.5M AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2006 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 51199 / Num. obs: 51199 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 62.3 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.09 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.48 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.199 / SU ML: 0.249 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.612 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.398 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.7→2.767 Å / Total num. of bins used: 20
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