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- PDB-6z9i: Escherichia coli D-2-deoxyribose-5-phosphate aldolase - N21K muta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6z9i | ||||||
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Title | Escherichia coli D-2-deoxyribose-5-phosphate aldolase - N21K mutant complex with reaction products | ||||||
![]() | Deoxyribose-phosphate aldolase | ||||||
![]() | LYASE / Aldolase / DERA | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Paakkonen, J. / Hakulinen, N. / Rouvinen, J. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.1 KB | Display | ![]() |
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PDB format | ![]() | 97.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 27 KB | Display | |
Data in CIF | ![]() | 43 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z9hC ![]() 6z9jC ![]() 1ktnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26930.033 Da / Num. of mol.: 2 / Mutation: N21K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() 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: ![]() ![]() References: UniProt: E2QLE1, UniProt: P0A6L0*PLUS, deoxyribose-phosphate aldolase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-G3H / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 4000, magnesium formate, TRIS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→19.27 Å / Num. obs: 39746 / % possible obs: 94.9 % / Redundancy: 3.57 % / Biso Wilson estimate: 14.88 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.125 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.86→1.97 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5999 / CC1/2: 0.71 / Rrim(I) all: 0.664 / % possible all: 90.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KTN Resolution: 1.86→19.27 Å / SU ML: 0.2079 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.3834 / Stereochemistry target values: GeoStd + Monomer Library
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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 mean: 17.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→19.27 Å
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Refine LS restraints |
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LS refinement shell |
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