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Yorodumi- PDB-4b7u: PLASMODIUM FALCIPARUM L-LACTATE DEHYDROGENASE COMPLEXED WITH BICINE -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b7u | |||||||||
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Title | PLASMODIUM FALCIPARUM L-LACTATE DEHYDROGENASE COMPLEXED WITH BICINE | |||||||||
Components | L-LACTATE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | |||||||||
Authors | Birkinshaw, R.W. / Brady, R.L. | |||||||||
Citation | Journal: To be Published Title: The Crystal Structure of Plasmodium Falciparum L- Lactate Dehydrogenase in Complex with a Novel Bicine Ligand Authors: Birkinshaw, R.W. / Brady, R.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b7u.cif.gz | 264.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b7u.ent.gz | 213 KB | Display | PDB format |
PDBx/mmJSON format | 4b7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b7u_validation.pdf.gz | 497.7 KB | Display | wwPDB validaton report |
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Full document | 4b7u_full_validation.pdf.gz | 506.5 KB | Display | |
Data in XML | 4b7u_validation.xml.gz | 52.8 KB | Display | |
Data in CIF | 4b7u_validation.cif.gz | 76.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/4b7u ftp://data.pdbj.org/pub/pdb/validation_reports/b7/4b7u | HTTPS FTP |
-Related structure data
Related structure data | 2x8lS S: Starting model for refinement |
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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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 34977.586 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Plasmid: PKK-233 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105 / References: UniProt: Q71T02, L-lactate dehydrogenase |
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-Non-polymers , 5 types, 860 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-BCN / #4: Chemical | ChemComp-MPD / ( | #5: Chemical | #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: 2.41 Å3/Da / Density % sol: 48.61 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 0.1 M BICINE PH 9, 22.5% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2010 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→49.09 Å / Num. obs: 115329 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 13.4 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.88→1.95 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X8L Resolution: 1.88→48.96 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→48.96 Å
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