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Yorodumi- PDB-3zh2: Structure of Plasmodium falciparum lactate dehydrogenase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zh2 | ||||||
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Title | Structure of Plasmodium falciparum lactate dehydrogenase in complex with a DNA aptamer | ||||||
Components |
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Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information Citric acid cycle (TCA cycle) / Gluconeogenesis / L-malate dehydrogenase (NAD+) activity / L-lactate dehydrogenase activity / glycolytic process / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cheung, Y.W. / Kwok, J. / Law, A.W.L. / Watt, R.M. / Kotaka, M. / Tanner, J.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structural Basis for Discriminatory Recognition of Plasmodium Lactate Dehydrogenase by a DNA Aptamer Authors: Cheung, Y.W. / Kwok, J. / Law, A.W.L. / Watt, R.M. / Kotaka, M. / Tanner, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zh2.cif.gz | 531.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zh2.ent.gz | 433.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zh2_validation.pdf.gz | 467.4 KB | Display | wwPDB validaton report |
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Full document | 3zh2_full_validation.pdf.gz | 492.9 KB | Display | |
Data in XML | 3zh2_validation.xml.gz | 53.9 KB | Display | |
Data in CIF | 3zh2_validation.cif.gz | 77.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/3zh2 ftp://data.pdbj.org/pub/pdb/validation_reports/zh/3zh2 | HTTPS FTP |
-Related structure data
Related structure data | 1ldgS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DG / Beg label comp-ID: DG / End auth comp-ID: DC / End label comp-ID: DC / Refine code: 4 / Auth seq-ID: 3 - 25 / Label seq-ID: 3 - 25
NCS oper:
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-Components
#1: Protein | Mass: 34148.715 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Strain: 3D7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76NM3, L-lactate dehydrogenase #2: DNA chain | Mass: 10758.911 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: 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: 4.08 Å3/Da / Density % sol: 69.87 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.2 M KCL, 0.1 M MAGNESIUM ACETATE, 0.05 M SODIUM CACODYLATE PH 6.5, 10% W/V PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 17, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 121507 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.5 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LDG Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.052 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.213 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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