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Yorodumi- PDB-1do8: CRYSTAL STRUCTURE OF A CLOSED FORM OF HUMAN MITOCHONDRIAL NAD(P)+... -
+Open data
-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 | ||||||
Components | MALIC ENZYME | ||||||
Keywords | OXIDOREDUCTASE / Oxidative Decarboxylase / Four domains: one with Rossmann fold / one with parallel alpha-beta fold / one mostly helical / and one mostly extended | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Yang, Z. / Floyd, D.L. / Loeber, G. / Tong, L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1do8.cif.gz | 472.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1do8.ent.gz | 382.2 KB | Display | PDB format |
PDBx/mmJSON format | 1do8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1do8_validation.pdf.gz | 954.6 KB | Display | wwPDB validaton report |
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Full document | 1do8_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1do8_validation.xml.gz | 55.1 KB | Display | |
Data in CIF | 1do8_validation.cif.gz | 83.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/1do8 ftp://data.pdbj.org/pub/pdb/validation_reports/do/1do8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is the tetramer in the asymmetric unit |
-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.) Homo sapiens (human) / Plasmid: PRH281 / Production host: Escherichia coli (E. coli) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.98 |
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 % |
-Processing
Software |
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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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