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- PDB-5jck: Structure and catalytic mechanism of monodehydroascorbate reducta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jck | ||||||
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Title | Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica | ||||||
![]() | Os09g0567300 protein | ||||||
![]() | HYDROLASE / hydrorase | ||||||
Function / homology | ![]() monodehydroascorbate reductase (NADH) / monodehydroascorbate reductase (NADH) activity / cellular oxidant detoxification / oxidoreductase activity, acting on NAD(P)H / peroxisomal matrix / flavin adenine dinucleotide binding / mRNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, A.K. / Kim, H.W. | ||||||
![]() | ![]() Title: Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica Authors: Park, A.K. / Kim, I.S. / Do, H. / Jeon, B.W. / Lee, C.W. / Roh, S.J. / Shin, S.C. / Park, H. / Kim, Y.S. / Kim, Y.H. / Yoon, H.S. / Lee, J.H. / Kim, H.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.3 KB | Display | ![]() |
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PDB format | ![]() | 81.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 970.7 KB | Display | ![]() |
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Full document | ![]() | 977.1 KB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jciC ![]() 5jclC ![]() 5jcmC ![]() 5jcnC ![]() 4h4qS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 48865.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Os09g0567300, Os09g0567300, OJ1155_H10.27, OSNPB_090567300 Production host: ![]() ![]() |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-NAD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris, lithium sulfate, PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97954 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 53422 / % possible obs: 99.7 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.145 / Χ2: 1.433 / Net I/av σ(I): 25.701 / Net I/σ(I): 5.7 / Num. measured all: 751594 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4H4Q Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.399 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.9 Å2 / Biso mean: 20.488 Å2 / Biso min: 8.3 Å2
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Refinement step | Cycle: final / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.997→2.049 Å / Total num. of bins used: 20
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