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Yorodumi- PDB-1m9h: Corynebacterium 2,5-DKGR A and Phe 22 replaced with Tyr (F22Y), L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m9h | ||||||
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Title | Corynebacterium 2,5-DKGR A and Phe 22 replaced with Tyr (F22Y), Lys 232 replaced with Gly (K232G), Arg 238 replaced with His (R238H)and Ala 272 replaced with Gly (A272G)in presence of NADH cofactor | ||||||
Components | 2,5-diketo-D-gluconic acid reductase A | ||||||
Keywords | OXIDOREDUCTASE / TIM-barrel | ||||||
Function / homology | Function and homology information 2,5-didehydrogluconate reductase (2-dehydro-L-gulonate-forming) / L-ascorbic acid biosynthetic process / oxidoreductase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Corynebacterium sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sanli, G. / Blaber, M. | ||||||
Citation | Journal: Protein Sci. / Year: 2004 Title: Structural alteration of cofactor specificity in Corynebacterium 2,5-diketo-D-gluconic acid reductase Authors: Sanli, G. / Banta, S. / Anderson, S. / Blaber, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m9h.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m9h.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 1m9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m9h_validation.pdf.gz | 684.9 KB | Display | wwPDB validaton report |
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Full document | 1m9h_full_validation.pdf.gz | 694.3 KB | Display | |
Data in XML | 1m9h_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1m9h_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/1m9h ftp://data.pdbj.org/pub/pdb/validation_reports/m9/1m9h | HTTPS FTP |
-Related structure data
Related structure data | 1a80S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30062.465 Da / Num. of mol.: 1 / Mutation: F22Y, K232G, R238H, A272G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium sp. (bacteria) / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) References: UniProt: P06632, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-NAD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.07 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: lithium sulfate monohydrate, hepes-sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2→40 Å / Num. all: 20178 / Num. obs: 17803 / % possible obs: 88.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 16.6 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.2 / % possible all: 83.3 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 27 Å / Num. obs: 18364 / % possible obs: 92.9 % / Num. measured all: 242073 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 83.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A80 Resolution: 2→40 Å / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / Stereochemistry target values: TRONRUD
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å /
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Refinement | *PLUS Lowest resolution: 27 Å / Rfactor Rwork: 0.214 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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