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Yorodumi- PDB-6k8c: Crystal structure of Helicobacter pylori folylpolyglutamate synthetase -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k8c | ||||||
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Title | Crystal structure of Helicobacter pylori folylpolyglutamate synthetase | ||||||
Components | Folylpolyglutamate synthase (FolC) | ||||||
Keywords | LIGASE / Folylpolyglutamate synthetase / Dihydropteroate synthetase / FolC / Bifunctional FolC | ||||||
Function / homology | Function and homology information dihydrofolate synthase / dihydrofolate synthase activity / folic acid-containing compound biosynthetic process / tetrahydrofolylpolyglutamate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95174964908 Å | ||||||
Authors | Park, J.S. / Han, B.W. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Crystals / Year: 2019 Title: Structural Analyses of Helicobacter Pylori FolC Conducting Glutamation in Folate Metabolism. Authors: Park, J.S. / Kim, H.S. / Park, S.H. / Park, M.S. / Kang, S.-M. / Kim, H.-J. / Han, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k8c.cif.gz | 112.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k8c.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 6k8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k8c_validation.pdf.gz | 452.9 KB | Display | wwPDB validaton report |
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Full document | 6k8c_full_validation.pdf.gz | 454.9 KB | Display | |
Data in XML | 6k8c_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 6k8c_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/6k8c ftp://data.pdbj.org/pub/pdb/validation_reports/k8/6k8c | 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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-Components
#1: Protein | Mass: 46013.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Gene: HP_1545 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O26070, tetrahydrofolate synthase |
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#2: Chemical | ChemComp-CIT / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, ammonium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97951 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 36178 / % possible obs: 98.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 33.8943026253 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Χ2: 1.048 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 4.24 / Num. unique obs: 1800 / CC1/2: 0.962 / Rpim(I) all: 0.169 / Rrim(I) all: 0.463 / Χ2: 1.093 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95174964908→29.9363061017 Å / SU ML: 0.189827748035 / Cross valid method: FREE R-VALUE / σ(F): 1.33481014704 / Phase error: 23.5747107896
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.2176693653 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95174964908→29.9363061017 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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