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- PDB-1do8: CRYSTAL STRUCTURE OF A CLOSED FORM OF HUMAN MITOCHONDRIAL NAD(P)+... -
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Basic information
Entry | Database: PDB / ID: 1do8 | ||||||
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Title | CRYSTAL STRUCTURE OF A CLOSED FORM OF HUMAN MITOCHONDRIAL NAD(P)+-DEPENDENT MALIC ENZYME | ||||||
![]() | MALIC ENZYME | ||||||
![]() | OXIDOREDUCTASE / Oxidative Decarboxylase / Four domains: one with Rossmann fold / one with parallel alpha-beta fold / one mostly helical / and one mostly extended | ||||||
Function / homology | ![]() malate dehydrogenase (oxaloacetate-decarboxylating) / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NAD+) activity / malic enzyme activity / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / malate metabolic process / Pyruvate metabolism / pyruvate metabolic process / Mitochondrial protein degradation ...malate dehydrogenase (oxaloacetate-decarboxylating) / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NAD+) activity / malic enzyme activity / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / malate metabolic process / Pyruvate metabolism / pyruvate metabolic process / Mitochondrial protein degradation / NAD binding / electron transfer activity / mitochondrial matrix / intracellular membrane-bounded organelle / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yang, Z. / Floyd, D.L. / Loeber, G. / Tong, L. | ||||||
![]() | ![]() Title: Structure of a closed form of human malic enzyme and implications for catalytic mechanism. Authors: Yang, Z. / Floyd, D.L. / Loeber, G. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 472.7 KB | Display | ![]() |
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PDB format | ![]() | 382.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is the tetramer in the asymmetric unit |
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Components
#1: Protein | Mass: 63893.168 Da / Num. of mol.: 4 / Mutation: METHIONINES REPLACED BY SELENOMETHIONINES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P23368, malate dehydrogenase (decarboxylating) #2: Chemical | ChemComp-OXL / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-NAD / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES 6-11% PEG20000 5% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 143000 / Num. obs: 136000 / % possible obs: 95 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.283 / % possible all: 87 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 87 % |
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Processing
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Refinement | Resolution: 2.2→20 Å / σ(F): 1 / σ(I): 2 / Stereochemistry target values: Engh&Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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