+Open data
-Basic information
Entry | Database: PDB / ID: 5nuf | ||||||
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Title | Cytosolic Malate Dehydrogenase 1 | ||||||
Components | Malate dehydrogenase 1, cytoplasmic | ||||||
Keywords | OXIDOREDUCTASE / Dehydrogenase / Malate/Oxaloacetate / NAD+ | ||||||
Function / homology | Function and homology information malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / plasmodesma / plant-type vacuole / oxaloacetate metabolic process / apoplast / NADH metabolic process / chloroplast stroma / response to zinc ion ...malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / plasmodesma / plant-type vacuole / oxaloacetate metabolic process / apoplast / NADH metabolic process / chloroplast stroma / response to zinc ion / tricarboxylic acid cycle / chloroplast / mRNA binding / extracellular region / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Young, D. / Messens, J. / Huang, J. / Reichheld, J.-P. | ||||||
Citation | Journal: J. Exp. Bot. / Year: 2018 Title: Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis. Authors: Huang, J. / Niazi, A.K. / Young, D. / Rosado, L.A. / Vertommen, D. / Bodra, N. / Abdelgawwad, M.R. / Vignols, F. / Wei, B. / Wahni, K. / Bashandy, T. / Bariat, L. / Van Breusegem, F. / ...Authors: Huang, J. / Niazi, A.K. / Young, D. / Rosado, L.A. / Vertommen, D. / Bodra, N. / Abdelgawwad, M.R. / Vignols, F. / Wei, B. / Wahni, K. / Bashandy, T. / Bariat, L. / Van Breusegem, F. / Messens, J. / Reichheld, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nuf.cif.gz | 222 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nuf.ent.gz | 175.8 KB | Display | PDB format |
PDBx/mmJSON format | 5nuf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nuf_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5nuf_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5nuf_validation.xml.gz | 44.3 KB | Display | |
Data in CIF | 5nuf_validation.cif.gz | 63.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/5nuf ftp://data.pdbj.org/pub/pdb/validation_reports/nu/5nuf | HTTPS FTP |
-Related structure data
Related structure data | 5nueC 4mdhS 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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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 35610.918 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell: Cytoplasmic / Gene: MDH1, At1g04410, F19P19.13 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P93819, malate dehydrogenase |
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-Non-polymers , 10 types, 570 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Chemical | #8: Chemical | ChemComp-EDO / #9: Chemical | #10: Chemical | ChemComp-FMT / | #11: 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: 2.66 Å3/Da / Density % sol: 53.85 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.18 M ammonium sulfate, 0.09 M sodium acetate trihydrate, 27% polyethylene glycol monomethyl ether 2000, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen cryogenic stream |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→43.67 Å / Num. obs: 110856 / % possible obs: 94.42 % / Redundancy: 6.7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.1717 / Rpim(I) all: 0.07035 / Rrim(I) all: 0.186 / Net I/σ(I): 10.15 |
Reflection shell | Resolution: 0.864→1.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.072 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.454 / Rpim(I) all: 0.6292 / Rrim(I) all: 1.252 / % possible all: 67.49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MDH Resolution: 1.8→43.67 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.8→43.67 Å
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LS refinement shell | Resolution: 1.8→1.864 Å / Rfactor Rfree: 0.3263 / Rfactor Rwork: 0.3142 |