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Yorodumi- PDB-6ovl: 2.1 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ovl | ||||||
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Title | 2.1 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with glyoxylate and NADP | ||||||
Components | Glyoxylate/hydroxypyruvate reductase A | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase (NADH) activity / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Vuksanovic, N. / Silvaggi, N.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: 2.1 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with glyoxylate and NADP Authors: Vuksanovic, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ovl.cif.gz | 211.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ovl.ent.gz | 170.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ovl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ovl_validation.pdf.gz | 767.4 KB | Display | wwPDB validaton report |
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Full document | 6ovl_full_validation.pdf.gz | 767.7 KB | Display | |
Data in XML | 6ovl_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 6ovl_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/6ovl ftp://data.pdbj.org/pub/pdb/validation_reports/ov/6ovl | HTTPS FTP |
-Related structure data
Related structure data | 6oxnC 6p35C 3kboS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36186.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) References: UniProt: W8T4J3, UniProt: P75913*PLUS, glyoxylate reductase (NADP+), hydroxypyruvate reductase |
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-Non-polymers , 7 types, 288 molecules
#2: Chemical | ChemComp-GOL / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-NAP / | #5: Chemical | ChemComp-GLV / | #6: Chemical | ChemComp-K / | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.4 M sodium phosphate monobasic/ potassium phosphate dibasic, 5 mM NADP, 100 mM sodium glyoxylate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→36.73 Å / Num. obs: 41974 / % possible obs: 99.09 % / Redundancy: 16.3 % / Biso Wilson estimate: 27.6828559215 Å2 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 2.1→2.175 Å / Num. unique obs: 3924 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KBO Resolution: 2.1→36.73 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.86 / 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: 2.1→36.73 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: -18.4953 Å / Origin y: 63.8768 Å / Origin z: -18.8906 Å
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Refinement TLS group | Selection details: all |