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Yorodumi- PDB-3ngj: Crystal structure of a putative deoxyribose-phosphate aldolase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ngj | ||||||
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Title | Crystal structure of a putative deoxyribose-phosphate aldolase from Entamoeba histolytica | ||||||
Components | Deoxyribose-phosphate aldolase | ||||||
Keywords | LYASE / DEOXYRIBOSE-PHOSPHATE ALDOLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Function and homology information deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / carbohydrate catabolic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative deoxyribose-phosphate aldolase from Entamoeba histolytica Authors: Abendroth, J. / Gardberg, A. / Staker, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ngj.cif.gz | 364.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ngj.ent.gz | 307.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ngj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/3ngj ftp://data.pdbj.org/pub/pdb/validation_reports/ng/3ngj | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25500.443 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_121800 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4M5C6 #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-ZN / #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: 2.21 Å3/Da / Density % sol: 44.3 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: MD PACT SCREEN CONDITION C12: 100MM HEPES, PH 7.0, 20% PEG 6000, 10MM ZNCL2. ENHIA.01205.A AT 42.7MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 97812 / Num. obs: 96738 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.1 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement, molecular replacement Resolution: 1.7→47.38 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.603 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→47.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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