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Yorodumi- PDB-5u4q: 1.5 Angstrom Resolution Crystal Structure of NAD-Dependent Epimer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u4q | ||||||
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Title | 1.5 Angstrom Resolution Crystal Structure of NAD-Dependent Epimerase from Klebsiella pneumoniae in Complex with NAD. | ||||||
Components | dTDP-glucose 4,6-dehydratase | ||||||
Keywords | LIPID BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / NAD-Dependent Epimerase / Lipid-Binding Protein | ||||||
Function / homology | NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : Function and homology information | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 1.5 Angstrom Resolution Crystal Structure of NAD-Dependent Epimerase from Klebsiella pneumoniae in Complex with NAD. Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u4q.cif.gz | 153.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u4q.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 5u4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u4q_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5u4q_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5u4q_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 5u4q_validation.cif.gz | 46.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/5u4q ftp://data.pdbj.org/pub/pdb/validation_reports/u4/5u4q | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38505.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: rffG_4, rffG_2, SAMEA2273684_00396, SAMEA2273712_05182 Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic References: UniProt: A0A169YGX7, dTDP-glucose 4,6-dehydratase #2: Chemical | #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: 2.14 Å3/Da / Density % sol: 42.5 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: Protein: 7.6 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: PEGs II (E10), 0.2M Ammonium sulfate, 20% (w/v) PEG 4000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2015 / Details: C(111) |
Radiation | Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 102114 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→29.21 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.588 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.08 / 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: 27.325 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→29.21 Å
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