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Yorodumi- PDB-6p35: 2.5 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p35 | ||||||
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Title | 2.5 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with 2-keto arginine 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 / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.495 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 | 6p35.cif.gz | 199.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p35.ent.gz | 161.5 KB | Display | PDB format |
PDBx/mmJSON format | 6p35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p35_validation.pdf.gz | 449.1 KB | Display | wwPDB validaton report |
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Full document | 6p35_full_validation.pdf.gz | 450.7 KB | Display | |
Data in XML | 6p35_validation.xml.gz | 2.4 KB | Display | |
Data in CIF | 6p35_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/6p35 ftp://data.pdbj.org/pub/pdb/validation_reports/p3/6p35 | HTTPS FTP |
-Related structure data
Related structure data | 6ovlC 6oxnC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35357.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain B / BL21-DE3) (bacteria) Strain: B / BL21-DE3 / Gene: ghrA, ECBD_2566 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A140NAE3, UniProt: P75913*PLUS, glyoxylate reductase (NADP+), hydroxypyruvate reductase |
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-Non-polymers , 5 types, 132 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NAP / | #5: Chemical | #6: 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 grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 17% PEG 3350, 0.2 M Li2SO4, 0.1 M BIS-TRIS pH 5.5, 1.8 mM NADP |
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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-G / Wavelength: 0.97872 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: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.495→45.78 Å / Num. obs: 25774 / % possible obs: 99.7 % / Redundancy: 1.8 % / Net I/σ(I): 29.51 |
Reflection shell | Resolution: 2.495→2.584 Å / Num. unique obs: 2492 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KBO Resolution: 2.495→45.78 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.495→45.78 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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