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Yorodumi- PDB-1pj4: Crystal structure of human mitochondrial NAD(P)+-dependent malic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pj4 | |||||||||
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Title | Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary complex with natural substrate malate, ATP, Mn++, and allosteric activator fumarate. | |||||||||
Components | NAD-dependent malic enzyme, mitochondrial | |||||||||
Keywords | OXIDOREDUCTASE / oxidative decarboxylase | |||||||||
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 / Citric acid cycle (TCA cycle) / malate metabolic process / 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 / Citric acid cycle (TCA cycle) / malate metabolic process / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Tao, X. / Yang, Z. / Tong, L. | |||||||||
Citation | Journal: Structure / Year: 2003 Title: Crystal structures of substrate complexes of malic enzyme and insights into the catalytic mechanism. Authors: Tao, X. / Yang, Z. / Tong, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pj4.cif.gz | 468.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pj4.ent.gz | 375.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pj4_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 1pj4_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 1pj4_validation.xml.gz | 90.4 KB | Display | |
Data in CIF | 1pj4_validation.cif.gz | 123.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/1pj4 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/1pj4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 63893.168 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ME2 / Production host: Escherichia coli (E. coli) References: UniProt: P23368, malate dehydrogenase (decarboxylating) |
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-Non-polymers , 5 types, 706 molecules
#2: Chemical | ChemComp-MLT / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-ATP / #5: Chemical | ChemComp-FUM / #6: 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: 2.73 Å3/Da / Density % sol: 54.94 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES (pH6.0), 10% PEG 20,000, 5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 32-ID / Wavelength: 0.9876 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 27, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9876 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 119748 / Num. obs: 119648 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.21 / % possible all: 94.2 |
Reflection | *PLUS Num. measured all: 379634 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.94 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.1139 Å2 / ksol: 0.369741 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2
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Refine analyze | Luzzati coordinate error free: 0.33 Å / Luzzati sigma a free: 0.25 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. reflection obs: 112846 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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