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Yorodumi- PDB-4nd5: Crystal structure of the lactate dehydrogenase from cryptosporidi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nd5 | |||||||||
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Title | Crystal structure of the lactate dehydrogenase from cryptosporidium parvum | |||||||||
Components | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / APOENZYME STRUCTURE | |||||||||
Function / homology | Function and homology information lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / nucleotide binding Similarity search - Function | |||||||||
Biological species | Cryptosporidium parvum (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Chattopadhyay, D. / Cook, W.J. | |||||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nd5.cif.gz | 230.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nd5.ent.gz | 187.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nd5_validation.pdf.gz | 417.1 KB | Display | wwPDB validaton report |
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Full document | 4nd5_full_validation.pdf.gz | 418.7 KB | Display | |
Data in XML | 4nd5_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 4nd5_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/4nd5 ftp://data.pdbj.org/pub/pdb/validation_reports/nd/4nd5 | HTTPS FTP |
-Related structure data
Related structure data | 4nd1C 4nd2C 4nd3C 4nd4C 2ewd C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33884.855 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd7_480, LDH1 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)PLYSS / References: UniProt: Q5CYZ2, L-lactate dehydrogenase #2: 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 16.5% PEG 2000, 0.1 M TRIS-HCL, 0.08% B-D-GLYCOPYRANOSIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9998 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 5, 2005 |
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: 2.1→20 Å / Num. obs: 100051 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.294 / % possible all: 64.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EWD 2ewd Resolution: 2.1→19.88 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.294 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.177 / 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: 53.287 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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