[English] 日本語
Yorodumi- PDB-6z9h: Escherichia coli D-2-deoxyribose-5-phosphate aldolase - C47V/G204... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z9h | ||||||
---|---|---|---|---|---|---|---|
Title | Escherichia coli D-2-deoxyribose-5-phosphate aldolase - C47V/G204A/S239D mutant | ||||||
Components | Deoxyribose-phosphate aldolase | ||||||
Keywords | LYASE / Aldolase / DERA | ||||||
Function / homology | Function and homology information deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / nucleobase-containing small molecule interconversion / carbohydrate catabolic process / lyase activity / DNA damage response / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Paakkonen, J. / Hakulinen, N. / Rouvinen, J. | ||||||
Funding support | Finland, 1items
| ||||||
Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2020 Title: Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods. Authors: Voutilainen, S. / Heinonen, M. / Andberg, M. / Jokinen, E. / Maaheimo, H. / Paakkonen, J. / Hakulinen, N. / Rouvinen, J. / Lahdesmaki, H. / Kaski, S. / Rousu, J. / Penttila, M. / Koivula, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6z9h.cif.gz | 148.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6z9h.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 6z9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/6z9h ftp://data.pdbj.org/pub/pdb/validation_reports/z9/6z9h | HTTPS FTP |
---|
-Related structure data
Related structure data | 6z9iC 6z9jC 1ktnS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28706.801 Da / Num. of mol.: 2 / Mutation: C47V/G204A/S239D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: deoC, A6592_04055, A9819_24930, AJ318_04090, AML35_20375, AWE53_009755, AWF59_004780, AWG90_001355, AZZ83_003140, B9M99_13055, BHF46_08905, BIU72_19175, BIZ41_21315, BK292_12675, BK296_03525, ...Gene: deoC, A6592_04055, A9819_24930, AJ318_04090, AML35_20375, AWE53_009755, AWF59_004780, AWG90_001355, AZZ83_003140, B9M99_13055, BHF46_08905, BIU72_19175, BIZ41_21315, BK292_12675, BK296_03525, BK375_05655, BON91_08010, BvCmsC61A_04176, BvCmsHHP001_01002, BvCmsKKP061_00143, BvCmsKSP045_01273, BvCmsKSP067_04018, BvCmsKSP076_01350, BvCmsNSP047_00091, BvCmsSINP022_00140, BZL69_04490, C4M78_04295, C7B08_10715, C7B18_26170, CDC27_23655, D2188_24830, D3P01_08005, D9D31_02570, D9E34_05115, D9G48_24275, D9I87_14825, D9I88_23755, D9K54_15785, DD762_00045, DND16_14490, DNQ45_13620, DTL90_19480, DTM45_25725, DU321_02660, DXT71_19415, E0L12_12025, E5S46_05005, E5S58_22595, E5S61_04910, EC382_07685, EL79_3891, EL80_3836, ELT23_13160, ELV08_18870, ELV15_04550, ELV28_15080, EQ825_04285, EQ830_02895, ERS085386_00787, EVY14_13465, EXX13_04350, EXX23_12990, EXX53_09895, EYY34_19360, FNJ83_01355, FV438_05665, FWK02_17600, FY127_22350, HMPREF3040_02396, NCTC10090_02419, NCTC7922_05561, NCTC9117_05294, NCTC9777_00681, NCTC9969_04462, PGD_03624, SAMEA3472056_01168, SAMEA3472108_04807, SAMEA3485101_00909, SAMEA3485113_03629, SAMEA3752559_04076, SAMEA3753300_03100, UC41_15640 Plasmid: pBAT4 / Production host: Escherichia coli (E. coli) References: UniProt: E2QLE1, UniProt: P0A6L0*PLUS, deoxyribose-phosphate aldolase #2: Chemical | #3: Chemical | ChemComp-FMT / | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.91 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350, magnesium formate, BIS-TRIS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9688 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9688 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→39.41 Å / Num. obs: 51138 / % possible obs: 96.9 % / Redundancy: 1.76 % / Biso Wilson estimate: 20.14 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.123 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.72→1.78 Å / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5131 / CC1/2: 0.503 / Rrim(I) all: 0.653 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KTN Resolution: 1.72→38.35 Å / SU ML: 0.2543 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4964 / Stereochemistry target values: GeoStd + Monomer Library
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→38.35 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|