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Yorodumi- PDB-6e85: 1.25 Angstrom Resolution Crystal Structure of 4-hydroxythreonine-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6.0E+85 | ||||||
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Title | 1.25 Angstrom Resolution Crystal Structure of 4-hydroxythreonine-4-phosphate Dehydrogenase from Klebsiella pneumoniae. | ||||||
Components | D-threonate 4-phosphate dehydrogenase | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / 4-hydroxythreonine-4-phosphate Dehydrogenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / 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 | 6e85.cif.gz | 330.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e85.ent.gz | 269.3 KB | Display | PDB format |
PDBx/mmJSON format | 6e85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e85_validation.pdf.gz | 471.9 KB | Display | wwPDB validaton report |
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Full document | 6e85_full_validation.pdf.gz | 476.7 KB | Display | |
Data in XML | 6e85_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 6e85_validation.cif.gz | 58.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/6e85 ftp://data.pdbj.org/pub/pdb/validation_reports/e8/6e85 | HTTPS FTP |
-Related structure data
Related structure data | 6dt3C 6duxC 6dvvC 6dxnC 6nauC 6nbgC 6ndiC 6wn5C 6wn8C 6x1lC 7rjjC 7tl5C 7tzpC 2hi1S 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35423.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Gene: pdxA, AN676_0302560, C4Z09_19135, C4Z14_08130, C4Z36_17000, C5Y00_08690, C5Y06_22400, CLQ72_17060, CVG30_05510 Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 (DE3) Magic References: UniProt: A0A1Y0PY16, 4-hydroxythreonine-4-phosphate dehydrogenase |
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-Non-polymers , 6 types, 964 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-POP / | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-CL / | #7: 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: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: 6.9 mg/ml, 0.01M Tris-HCl pH 8.3; Screen: Classics II (G2), 0.2M Lithium sulfate, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350; |
-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 300 mm CCD / Detector: CCD / Date: Jul 24, 2018 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→30 Å / Num. obs: 177342 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.06 / Rsym value: 0.053 / Χ2: 1 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8637 / CC1/2: 0.8 / Rpim(I) all: 0.349 / Rrim(I) all: 0.654 / Rsym value: 0.549 / Χ2: 0.999 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HI1 Resolution: 1.25→29.67 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.22 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.035 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.874 Å2
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Refinement step | Cycle: 1 / Resolution: 1.25→29.67 Å
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Refine LS restraints |
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