+Open data
-Basic information
Entry | Database: PDB / ID: 6daq | |||||||||||||||
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Title | PhdJ bound to substrate intermediate | |||||||||||||||
Components | (PhdJ) x 2 | |||||||||||||||
Keywords | LYASE / aldolase | |||||||||||||||
Function / homology | DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel / lyase activity / PhdJ Function and homology information | |||||||||||||||
Biological species | Mycobacterium vanbaalenii (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | |||||||||||||||
Authors | Medellin, B.P. / LeVieux, J.A. / Zhang, Y.J. / Whitman, C.P. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Biochemistry / Year: 2018 Title: Structural Characterization of the Hydratase-Aldolases, NahE and PhdJ: Implications for the Specificity, Catalysis, and N-Acetylneuraminate Lyase Subgroup of the Aldolase Superfamily. Authors: LeVieux, J.A. / Medellin, B. / Johnson Jr., W.H. / Erwin, K. / Li, W. / Johnson, I.A. / Zhang, Y.J. / Whitman, C.P. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6daq.cif.gz | 271.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6daq.ent.gz | 226.1 KB | Display | PDB format |
PDBx/mmJSON format | 6daq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6daq_validation.pdf.gz | 451.1 KB | Display | wwPDB validaton report |
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Full document | 6daq_full_validation.pdf.gz | 462.2 KB | Display | |
Data in XML | 6daq_validation.xml.gz | 58.8 KB | Display | |
Data in CIF | 6daq_validation.cif.gz | 86.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/6daq ftp://data.pdbj.org/pub/pdb/validation_reports/da/6daq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36231.863 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium vanbaalenii (bacteria) / Gene: phdJ / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress / References: UniProt: Q6H2K0 #2: Protein | | Mass: 36099.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium vanbaalenii (bacteria) / Gene: phdJ / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress / References: UniProt: Q6H2K0 #3: 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: 2.17 Å3/Da / Density % sol: 43.33 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M MES at pH 7-7.5 and 22-25% in PEG 3350 / PH range: 7-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.99-1.5 | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2015 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2→50 Å / Num. obs: 77204 / % possible obs: 93.5 % / Redundancy: 3.6 % / Net I/σ(I): 14 | |||||||||
Reflection shell | Resolution: 2→2.07 Å |
-Processing
Software |
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Refinement | Resolution: 2→45.29 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→45.29 Å
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Refine LS restraints |
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LS refinement shell |
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