+Open data
-Basic information
Entry | Database: PDB / ID: 4xbk | ||||||
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Title | 2-deoxyribose-5-phosphate aldolase from Lactobacillus brevis | ||||||
Components | Deoxyribose-phosphate aldolase | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / carbohydrate catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Lactobacillus brevis ATCC 14869 = DSM 20054 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.951 Å | ||||||
Authors | Jiao, X.-C. / Pan, J. / Xu, G.-C. / Kong, X.-D. / Chen, Q. / Zhang, Z.-J. / Xu, J.-H. | ||||||
Funding support | China, 1items
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Citation | Journal: Catalysis Science And Technology / Year: 2015 Title: Efficient synthesis of a statin precursor in high space-time yield by a new aldehyde-tolerant aldolase identified from Lactobacillus brevis Authors: Jiao, X.-C. / Pan, J. / Xu, G.-C. / Kong, X.-D. / Chen, Q. / Zhang, Z.-J. / Xu, J.-H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xbk.cif.gz | 106.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xbk.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 4xbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/4xbk ftp://data.pdbj.org/pub/pdb/validation_reports/xb/4xbk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28049.650 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus brevis ATCC 14869 = DSM 20054 (bacteria) Strain: ATCC 14869 = DSM 20054 / Gene: deoC, HMPREF0495_01319 / Production host: Escherichia coli (E. coli) / References: UniProt: U2PI02, deoxyribose-phosphate aldolase #2: Chemical | #3: 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: 2.5 Å3/Da / Density % sol: 50.82 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: ammonium acetate, sodium acetate / PH range: 4.3-5.4 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 10, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→50 Å / Num. obs: 42101 / % possible obs: 99.9 % / Redundancy: 27.5 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.02 / Rrim(I) all: 0.105 / Χ2: 1.018 / Net I/av σ(I): 28.663 / Net I/σ(I): 15.1 / Num. measured all: 1158340 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.951→44.898 Å / FOM work R set: 0.8825 / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 17.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.55 Å2 / Biso mean: 29.89 Å2 / Biso min: 15.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.951→44.898 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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