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Yorodumi- PDB-6nau: 1.55 Angstrom Resolution Crystal Structure of 6-phosphogluconolac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nau | ||||||
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Title | 1.55 Angstrom Resolution Crystal Structure of 6-phosphogluconolactonase from Klebsiella pneumoniae | ||||||
Components | 6-phosphogluconolactonase | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / 6-phosphogluconolactonase | ||||||
Function / homology | Function and homology information 6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt / glucose metabolic process Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Pshenychnyi, S. / Dubrovska, I. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Microbiol Resour Announc / Year: 2023 Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae. Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nau.cif.gz | 262.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nau.ent.gz | 207.7 KB | Display | PDB format |
PDBx/mmJSON format | 6nau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/6nau ftp://data.pdbj.org/pub/pdb/validation_reports/na/6nau | HTTPS FTP |
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-Related structure data
Related structure data | 6dt3C 6duxC 6dvvC 6dxnC 6e85C 6nbgC 6ndiC 6wn5C 6wn8C 6x1lC 7rjjC 7tl5C 7tzpC 4qrjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 36462.789 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Gene: ybhE, pgl, NCTC9504_04578 / Plasmid: pMCSG53 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2X3FDC7, UniProt: A6T6J6*PLUS, 6-phosphogluconolactonase #2: Chemical | ChemComp-B3P / #3: Chemical | ChemComp-CL / #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: 2.13 Å3/Da / Density % sol: 42.3 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 9.8 mg/ml, 0.01M Tris-HCl pH 8.3, Screen: PACT (F6), 0.2M Sodium formate, 0.1M Bis-Tris propane pH 6.5, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2018 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 138516 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.035 / Rrim(I) all: 0.106 / Rsym value: 0.1 / Χ2: 1.005 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 6923 / CC1/2: 0.861 / Rpim(I) all: 0.258 / Rrim(I) all: 0.757 / Rsym value: 0.711 / Χ2: 1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QRJ Resolution: 1.55→29.33 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.283 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.069 / 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: 12.521 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→29.33 Å
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Refine LS restraints |
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