+Open data
-Basic information
Entry | Database: PDB / ID: 7bsk | |||||||||
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Title | Crystal structure of human ME2 R67Q mutant | |||||||||
Components | NAD-dependent malic enzyme, mitochondrial | |||||||||
Keywords | HYDROLASE / malate dehydrogenase / NAD-dependent malic enzyme | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | |||||||||
Authors | Chen, W.L. / Tai, S.C. / Hung, H.C. / Ho, M.C. | |||||||||
Funding support | Taiwan, 2items
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Citation | Journal: Iscience / Year: 2021 Title: Single nucleotide variants lead to dysregulation of the human mitochondrial NAD(P) + -dependent malic enzyme. Authors: Hsieh, J.Y. / Yang, H.P. / Tewary, S.K. / Cheng, H.C. / Liu, Y.L. / Tai, S.C. / Chen, W.L. / Hsu, C.H. / Huang, T.J. / Chou, C.J. / Huang, Y.N. / Peng, C.T. / Ho, M.C. / Liu, G.Y. / Hung, H.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bsk.cif.gz | 230.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bsk.ent.gz | 184.1 KB | Display | PDB format |
PDBx/mmJSON format | 7bsk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bsk_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7bsk_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7bsk_validation.xml.gz | 42 KB | Display | |
Data in CIF | 7bsk_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/7bsk ftp://data.pdbj.org/pub/pdb/validation_reports/bs/7bsk | HTTPS FTP |
-Related structure data
Related structure data | 7bsjC 7bslC 1eflS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 63476.922 Da / Num. of mol.: 2 / Mutation: R67Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ME2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P23368, malate dehydrogenase (oxaloacetate-decarboxylating) #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.5 / Details: PEG20000 6.575% MPD(v/v) 5% MES (pH=6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 6, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.54→30 Å / Num. obs: 44503 / % possible obs: 99 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.036 / Rrim(I) all: 0.08 / Χ2: 0.963 / Net I/σ(I): 10.1 / Num. measured all: 213224 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1efl Resolution: 2.55→29.48 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.871 / SU B: 13.293 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.143 / ESU R Free: 0.36 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.57 Å2 / Biso mean: 40.933 Å2 / Biso min: 18.48 Å2
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Refinement step | Cycle: final / Resolution: 2.55→29.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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