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Yorodumi- PDB-2fn7: Crystal structure of the lactate dehydrogenase from cryptosporidi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fn7 | |||||||||
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Title | Crystal structure of the lactate dehydrogenase from cryptosporidium parvum complexed with substrate (lactic acid) and cofactor (b-nicotinamide adenine dinucleotide) | |||||||||
Components | Lactate Dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / Enzyme_substrate_cofactor complex | |||||||||
Function / homology | Function and homology information carboxylic acid metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding Similarity search - Function | |||||||||
Biological species | Cryptosporidium parvum (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Senkovich, O.A. / Chattopadhyay, D. | |||||||||
Citation | Journal: To be Published Title: Structure of cryptosporidium parvum lactate dehydrogenase in complex with substrates and cofactors Authors: Senkovich, O.A. / Chattopadhyay, D. | |||||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ALTHOUGH LDH ENZYMES ARE KNOWN TO BE FUNCTIONAL AS TETRAMERS AND IN SOLUTION C. PARVUM LDH IS TETRAMERIC, THIS ENZYME WAS EARLIER REPORTED TO BE DIMERIC [REF: MADERN D., CAI X, ABRAHAMSEN MS, ZHU G. (2004) "EVOLUTION OF CRYPTOSPORIDIUM PARVUM LACTATE DEHYDROGENASE FROM MALATE DEHYDROGENASE BY A VERY RECENT EVENT OF GENE DUPLICATION" MOL. BIOL. EVOL. 21, 489-497]. | |||||||||
Remark 999 | SEQUENCE PEPTIDE SEQUENCE FOR THIS ENTRY WAS TRANSLATED FROM DNA SEQUENCING OF ACTUAL CLONE USED ...SEQUENCE PEPTIDE SEQUENCE FOR THIS ENTRY WAS TRANSLATED FROM DNA SEQUENCING OF ACTUAL CLONE USED FOR PROTEIN EXPRESSION. AUTHORS DO NOT KNOW IF THE SEQUENCE DIFFERENCES ARE PCR ERRORS OR MUTATIONS CORRESPONDING DNA POLYMORPHISM OR THERE WERE ERRORS IN PROTEIN DATABASE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fn7.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fn7.ent.gz | 105.7 KB | Display | PDB format |
PDBx/mmJSON format | 2fn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/2fn7 ftp://data.pdbj.org/pub/pdb/validation_reports/fn/2fn7 | HTTPS FTP |
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-Related structure data
Related structure data | 2ewd 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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2 |
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Unit cell |
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Details | At present there is no evidence whether this enzyme functions as a tetramer or as a dimer (see related entry 2FM3) |
-Components
#1: Protein | Mass: 33884.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: LDH1 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3)PLYSS References: GenBank: 10444017, UniProt: Q5CYZ2*PLUS, L-lactate dehydrogenase #2: Chemical | #3: Chemical | ChemComp-LAC / | #4: Chemical | #5: 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: 3.61 Å3/Da / Density % sol: 65.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.75 Details: 1.65 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9998 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 1, 2004 / Details: mirrors |
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: 2.3→50 Å / Num. all: 50645 / Num. obs: 50645 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.065 / Χ2: 0.584 |
Reflection shell | Resolution: 2.3→2.37 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.274 / Num. unique all: 4988 / Χ2: 0.372 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2EWD 2ewd Resolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 43.812 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.846 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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