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Yorodumi- PDB-5zix: Crystal structure of Ketopantoate reductase from Pseudomonas aeru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zix | ||||||
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Title | Crystal structure of Ketopantoate reductase from Pseudomonas aeruginosa bound to NADP+ | ||||||
Components | Probable 2-dehydropantoate 2-reductase | ||||||
Keywords | OXIDOREDUCTASE / 2-dehydropantoate 2-reductase / panthothenate biosythesis pathway / NADP+ / NADPH | ||||||
Function / homology | Function and homology information 2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process / NADP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å | ||||||
Authors | Khanppnavar, B. / Datta, S. | ||||||
Funding support | India, 1items
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Citation | Journal: Biochim Biophys Acta Gen Subj / Year: 2019 Title: Genome-wide survey and crystallographic analysis suggests a role for both horizontal gene transfer and duplication in pantothenate biosynthesis pathways. Authors: Khanppnavar, B. / Chatterjee, R. / Choudhury, G.B. / Datta, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zix.cif.gz | 374 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zix.ent.gz | 307.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/5zix ftp://data.pdbj.org/pub/pdb/validation_reports/zi/5zix | HTTPS FTP |
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-Related structure data
Related structure data | 5zikC 1ks9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33105.621 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: panE, PA4397 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HW09, 2-dehydropantoate 2-reductase #2: Chemical | #3: Chemical | #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: 3.41 Å3/Da / Density % sol: 63.91 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion / pH: 7.5 Details: 1.3M Sodium-Potassium-Tartarate, 50mM BICINE pH 7.5 PH range: 7.0-8.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→48.15 Å / Num. obs: 44028 / % possible obs: 98.9 % / Redundancy: 14.7 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.02 / Rrim(I) all: 0.078 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.56→2.6 Å / Redundancy: 15 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1735 / CC1/2: 0.737 / Rpim(I) all: 0.504 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KS9 Resolution: 2.57→40.598 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 26.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.57→40.598 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 32.7224 Å / Origin y: 53.6557 Å / Origin z: 21.706 Å
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Refinement TLS group | Selection details: all |