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- PDB-4nd4: Crystal structure of the lactate dehydrogenase from cryptosporidi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nd4 | ||||||||||||
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Title | Crystal structure of the lactate dehydrogenase from cryptosporidium parvum complexed with substrate (pyruvic acid) and cofactor (b-nicotinamide adenine dinucleotide) | ||||||||||||
![]() | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | ||||||||||||
![]() | OXIDOREDUCTASE / Rossmann fold / Dehydrogenase / NAD binding | ||||||||||||
Function / homology | ![]() lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / nucleotide binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Chattopadhyay, D. / Cook, W.J. | ||||||||||||
![]() | ![]() Title: Biochemical and structural characterization of Cryptosporidium parvum Lactate dehydrogenase. Authors: Cook, W.J. / Senkovich, O. / Hernandez, A. / Speed, H. / Chattopadhyay, D. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.9 KB | Display | ![]() |
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PDB format | ![]() | 108.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1012.7 KB | Display | ![]() |
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Full document | ![]() | 1016.3 KB | Display | |
Data in XML | ![]() | 26.8 KB | Display | |
Data in CIF | ![]() | 37.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nd1C ![]() 4nd2C ![]() 4nd3C ![]() 4nd5C ![]() 2ewd C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33884.855 Da / Num. of mol.: 2 / Fragment: unp residues 17-337 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | PEPTIDE SEQUENCE FOR THIS ENTRY WAS TRANSLATED FROM DNA SEQUENCING OF ACTUAL CLONE USED FOR PROTEIN ...PEPTIDE SEQUENCE FOR THIS ENTRY WAS TRANSLATED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: The protein was incubated with 1 mM pyruvate and 100 uM APAD+ for 1 hour on ice prior to crystallization. Reservoir solution was 1.45-1.65 M ammonium sulfate in 0.1 M sodium cacodylate, pH 7. ...Details: The protein was incubated with 1 mM pyruvate and 100 uM APAD+ for 1 hour on ice prior to crystallization. Reservoir solution was 1.45-1.65 M ammonium sulfate in 0.1 M sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 2, 2004 |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 50964 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.303 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 2EWD ![]() 2ewd Resolution: 2.2→49.64 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.589 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.169 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.329 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.64 Å
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Refine LS restraints |
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