+Open data
-Basic information
Entry | Database: PDB / ID: 6ioy | |||||||||
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Title | Crystal structure of Porphyromonas gingivalis acetate kinase | |||||||||
Components | Acetate kinase | |||||||||
Keywords | TRANSFERASE / Porphyromonas gingivalis / acetate kinase / ATP / essential gene | |||||||||
Function / homology | Function and homology information acetate kinase / organic acid metabolic process / acetate kinase activity / acetyl-CoA biosynthetic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Porphyromonas gingivalis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | |||||||||
Authors | Kezuka, Y. / Yoshida, Y. / Nonaka, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J Oral Microbiol / Year: 2019 Title: Characterization of the phosphotransacetylase-acetate kinase pathway for ATP production inPorphyromonas gingivalis. Authors: Yoshida, Y. / Sato, M. / Nonaka, T. / Hasegawa, Y. / Kezuka, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ioy.cif.gz | 325.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ioy.ent.gz | 263.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ioy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ioy_validation.pdf.gz | 470.8 KB | Display | wwPDB validaton report |
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Full document | 6ioy_full_validation.pdf.gz | 477.6 KB | Display | |
Data in XML | 6ioy_validation.xml.gz | 63 KB | Display | |
Data in CIF | 6ioy_validation.cif.gz | 92.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/6ioy ftp://data.pdbj.org/pub/pdb/validation_reports/io/6ioy | HTTPS FTP |
-Related structure data
Related structure data | 6iowC 6ioxC 2iirS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 43765.555 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) (bacteria) Strain: ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561 Gene: ackA, PGN_1178 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2RK02, acetate kinase #2: Chemical | #3: Chemical | ChemComp-SO4 / #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: 2.39 Å3/Da / Density % sol: 48.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M lithium sulfate monohydrate, 0.1 M Tris/HCl (pH 8.5), and 24% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→53.4 Å / Num. obs: 120952 / % possible obs: 99.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.78 / Num. unique obs: 5602 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IIR Resolution: 1.94→53.4 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.435 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.147 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.041 Å2
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Refinement step | Cycle: 1 / Resolution: 1.94→53.4 Å
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Refine LS restraints |
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