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Yorodumi- PDB-5jcm: Structure and catalytic mechanism of monodehydroascorbate reducta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jcm | |||||||||
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Title | Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica | |||||||||
Components | Os09g0567300 protein | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information monodehydroascorbate reductase (NADH) / monodehydroascorbate reductase (NADH) activity / oxidoreductase activity, acting on NAD(P)H / cellular oxidant detoxification / peroxisomal matrix / flavin adenine dinucleotide binding / mRNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Park, A.K. / Kim, H.W. | |||||||||
Citation | Journal: Sci Rep / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jcm.cif.gz | 196.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jcm.ent.gz | 152.3 KB | Display | PDB format |
PDBx/mmJSON format | 5jcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jcm_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5jcm_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5jcm_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 5jcm_validation.cif.gz | 59.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/5jcm ftp://data.pdbj.org/pub/pdb/validation_reports/jc/5jcm | HTTPS FTP |
-Related structure data
Related structure data | 5jciC 5jckC 5jclC 5jcnC 4h4qS C: citing same article (ref.) 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: 48619.055 Da / Num. of mol.: 2 / Fragment: UNP residues 4-435 / Mutation: Y349F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: Os09g0567300, Os09g0567300, OJ1155_H10.27, OSNPB_090567300 Production host: Escherichia coli (E. coli) / References: UniProt: Q652L6 #2: Chemical | #3: Chemical | #4: Sugar | #5: 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: 2.38 Å3/Da / Density % sol: 48.41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris, ammonium acetate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97954 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 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: 1.9→71.52 Å / Num. obs: 69512 / % possible obs: 99.3 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Rrim(I) all: 0.107 / Χ2: 2.568 / Net I/av σ(I): 52.35 / Net I/σ(I): 10.8 / Num. measured all: 982181 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4H4Q Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.387 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.144 / 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: 122.3 Å2 / Biso mean: 39.303 Å2 / Biso min: 6.52 Å2
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Refinement step | Cycle: final / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.902→1.951 Å / Total num. of bins used: 20
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