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- PDB-7ne2: Crystal structure of class I SFP aldolase YihT from Salmonella en... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ne2 | ||||||
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Title | Crystal structure of class I SFP aldolase YihT from Salmonella enterica with SFP/ DHAP (Schiff base complex with active site Lys193) | ||||||
![]() | Sulfofructosephosphate aldolase | ||||||
![]() | LYASE / sulfoglycolysis / SFP aldolase / class I / DHAP / sulfolactaldehyde / dihydroxyacetone phosphate | ||||||
Function / homology | ![]() sulfofructosephosphate aldolase / 6-deoxy-6-sulfofructose-1-phosphate aldolase activity / 6-sulfoquinovose(1-) catabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharma, M. / Davies, G.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis. Authors: Sharma, M. / Abayakoon, P. / Epa, R. / Jin, Y. / Lingford, J.P. / Shimada, T. / Nakano, M. / Mui, J.W. / Ishihama, A. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.1 KB | Display | ![]() |
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PDB format | ![]() | 201.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 51.4 KB | Display | |
Data in CIF | ![]() | 76.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ag1C ![]() 7ag4C ![]() 7ag6C ![]() 7ag7SC ![]() 7aghC ![]() 7agkC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 34076.262 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: A0N81_18250, A3M31_18775, A6870_09715, A6898_11780, A7749_21790, A7F95_15550, AIO56_15225, AIY46_16340, AL463_07200, AUD13_20420, AWT52_20455, AWU43_13980, AXB23_12525, B1Q59_20525, B5654_ ...Gene: A0N81_18250, A3M31_18775, A6870_09715, A6898_11780, A7749_21790, A7F95_15550, AIO56_15225, AIY46_16340, AL463_07200, AUD13_20420, AWT52_20455, AWU43_13980, AXB23_12525, B1Q59_20525, B5654_18495, B9864_14245, BH399_15915, BM489_16210, BUX38_13710, BWB44_15835, BZG86_17325, BZG97_21310, C0X54_15110, CF411_19890, CGY76_15895, CIU94_12215, CJT17_15765, CKB50_07315, CKU74_14590, COP74_11865, COQ67_11805, CQW68_17310, CRH85_14725, CRQ37_15620, CRX97_18560, CS198_12645, CSK90_20940, CTB03_19360, D0C46_16695, D1239_15905, D3346_03620, D3P91_16440, D5403_16535, D5563_18085, D5K09_17370, D5K19_15290, D5S75_07410, D5T72_18210, D5U49_16110, D5U61_18460, D5U63_11355, D6093_17370, D6272_19205, D6518_20345, D6570_13930, D6969_14660, D6E28_04120, D6E86_17625, D6F20_16795, D6F49_14185, D6G02_17665, D6G26_10200, D6G47_17665, D6G76_19295, D6H24_18045, D6H57_18255, D6I51_13955, D6I58_08830, D6J18_10675, D6N21_14905, D6N55_08625, D6O25_17540, D6O30_15095, D6Y46_16705, D7B84_19925, D7B88_17660, D7C05_16595, D7C06_21680, D7C84_14020, D7C85_15860, D7D21_15750, D7D22_05990, D7D38_09665, D7D43_21660, D7E22_19080, D7E26_17595, D7E90_22935, D7F69_17605, D7G05_16290, D7G28_16865, D7G59_21240, D7J34_06690, D7L19_20755, D7M32_23435, D7T23_13960, D7U23_11360, D7U29_12545, D7V14_12170, D7V56_03055, D7W03_19080, D7W42_15665, D7W92_17045, D7X02_18505, D8I75_22320, D8I93_09135, D8N07_15105, D8N11_16775, D8N46_13960, D8N55_16780, D8O41_20680, D8P26_14535, D8P48_20440, D8P50_21965, D8P66_11165, D8T80_18610, D8U57_08880, D8V04_12990, D8V52_15680, D8W17_18845, D8W37_13540, D8X82_11100, D8X94_09915, D9788_20490, D9789_20795, D9813_16860, D9893_11870, D9904_16025, D9908_21180, D9A34_21035, D9A73_12625, D9B25_17115, D9B94_19645, D9B97_15535, D9N56_15950, D9N82_18885, D9R37_17245, D9R54_15605, DKH31_16885, DKT79_16205, DLG27_11245, DLG46_06205, DLG52_07510, DLG63_07605, DLG68_10135, DLO13_17295, DLO43_18780, DM517_15195, DM524_16185, DM771_11020, DO307_21625, DP889_19510, DPH90_12840, DPI33_15970, DQT99_17410, DS006_04045, DSC90_17425, DT233_14295, DTC77_09285, DTD68_12010, DTS56_10715, DV697_20955, DWE28_16300, DXG53_11555, DXJ54_22650, DXN62_09570, DXS05_10875, EA021_14685, EA079_18825, EA089_19020, EA474_08655, EA495_19590, EA530_18665, EA547_20545, EA580_19185, EA608_19155, EA613_20370, EA865_08835, EA919_10115, EAA74_11055, EAB27_13270, EAB35_16100, EAB61_09075, EAB95_19485, EAC03_16205, EAC50_16505, EAC62_17350, EAC94_18900, EAD37_15045, EAD40_09145, EAD57_13665, EAD76_19515, EAM93_17780, EAN15_16450, EAN28_13585, EAP40_16925, EAP69_20610, EAP86_19400, EAT69_18110, EAT75_16760, EAT82_14950, EAU16_09940, EAU32_20705, EAU35_15685, EAU46_12835, EAU53_10110, EAU58_12765, EAU70_20970, EAV62_11145, EAW74_11570, EAW95_17755, EAX13_03905, EAX14_14635, EAX36_11700, EAX53_13770, EBB31_16095, EBF85_18205, EBG44_16225, EBG45_13980, EBG75_07135, EBH58_15795, EBH87_22355, EBI58_18035, EE513_15450, EF325_19645, EF388_12305, EF393_20830, EF628_09690, EF991_17315, EFC63_19880, EFC67_20365, EFE59_16535, EFG85_09970, EFH54_15625, EFH94_15335, EFJ16_17715, EFY29_17600, EFZ26_04800, EFZ60_09705, EG093_16475, EG164_13955, EG208_16115, EG454_09425, EG623_11865, EG641_09825, EG692_19510, EG762_13995, EG767_06865, EG904_07125, EG952_08925, EG958_15370, EGA35_15790, EGA57_09435, EGC01_19260, EGC99_17865, EGD06_09555, EGD07_07640, EGD31_09160, EGD39_14760, EGI61_15585, EGS29_19525, EGY78_10120, EGZ16_20780, EGZ23_10235, EH065_16465, EH070_09515, EH342_16890, EH378_03350, EH386_15285, EH444_09295, EHA32_16515, EHA97_05130, EHG07_19400, EHG48_13385, EHG76_05255, EHN34_10355, EHN57_18120, EHN63_15685, EHN69_20070, EHN71_15015, EHN74_20955, EHN75_15295, EHO38_16865, EHT01_15035, EHT24_15825, EHU01_19845, EHU13_18495, EHZ75_17125, EI217_12345, EID62_19165, EIM38_09355, EIN80_15985, EIP55_14465, EIQ89_18750, EIR18_16870, EIR57_14645, EIR68_20810, EIR69_10290, EIR74_09395, EIR86_11165, EIS08_13390, EIS13_04610, EIU76_04060, EIU90_06585, EIV01_12260, EIW14_04360, EIW18_14780, F0673_17300, F0Y85_06995, F1H08_17590, F2162_17330, F2262_17185, F2D15_19045, F3368_19600, F3E97_16225, F3Z27_11460, F6G43_17665, F6H70_17780, F7365_11585, F7450_19930, F7M71_12365, F8658_14000, FE26_19770, FJR52_18110, FLX20_17775, FQR50_10080, FR099_15765, FRH21_16835, FRK18_12280, FY665_16255, FZ154_17610, FZ547_18070, GB762_17280, GC435_07645, GC879_16555, GCA81_13885, GCH85_20920, GCR52_14595, IX01_17020, R929_17375 Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: A0A0W4SFQ6, sulfofructosephosphate aldolase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30% Jeffamine M-600 v/v pH 7 and 0.1 M HEPES buffer pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 15, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→42.5 Å / Num. obs: 183409 / % possible obs: 96.6 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.025 / Rrim(I) all: 0.049 / Net I/σ(I): 12.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7AG7 Resolution: 1.5→42.48 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.662 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.77 Å2 / Biso mean: 24.034 Å2 / Biso min: 13.75 Å2
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Refinement step | Cycle: final / Resolution: 1.5→42.48 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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