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Yorodumi- PDB-1gz4: molecular mechanism of the regulation of human mitochondrial NAD(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gz4 | |||||||||
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Title | molecular mechanism of the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate | |||||||||
Components | NAD-DEPENDENT MALIC ENZYME | |||||||||
Keywords | OXIDOREDUCTASE / ALLOSTERIC REGULATION / ENERGY METABOLISM / KINETICS | |||||||||
Function / homology | Function and homology information malate dehydrogenase (oxaloacetate-decarboxylating) / malate dehydrogenase (decarboxylating) (NAD+) activity / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / Citric acid cycle (TCA cycle) / malate metabolic process / pyruvate metabolic process / NAD binding ...malate dehydrogenase (oxaloacetate-decarboxylating) / malate dehydrogenase (decarboxylating) (NAD+) activity / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / Citric acid cycle (TCA cycle) / malate metabolic process / pyruvate metabolic process / 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: 2.2 Å | |||||||||
Authors | Yang, Z. / Lanks, C.W. / Tong, L. | |||||||||
Citation | Journal: Structure / Year: 2002 Title: Molecular Mechanism for the Regulation of Human Mitochondrial Nad(P)(+)-Dependent Malic Enzyme by ATP and Fumarate Authors: Yang, Z. / Lanks, C.W. / Tong, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gz4.cif.gz | 452.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gz4.ent.gz | 370.8 KB | Display | PDB format |
PDBx/mmJSON format | 1gz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/1gz4 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/1gz4 | HTTPS FTP |
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-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: 62552.656 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Organelle: MITOCHONDRION References: UniProt: P23368, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) |
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-Non-polymers , 5 types, 592 molecules
#2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-TTN / #4: Chemical | ChemComp-MN / #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: 2.78 Å3/Da / Density % sol: 55.76 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: 10% PEG20K, PH6.0 MES, 5% MPD, pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.97 |
Detector | Date: Jun 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 123880 / % possible obs: 95 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 10 / % possible all: 82 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 95 % / Num. measured all: 379495 |
Reflection shell | *PLUS % possible obs: 82 % / Rmerge(I) obs: 0.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DO8_D Resolution: 2.2→20 Å / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.3 Å2 / ksol: 0.44 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.21 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 50
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.271 / Rfactor Rwork: 0.244 |