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Open data
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Basic information
Entry | Database: PDB / ID: 6p85 | ||||||
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Title | E.coli LpxD in complex with compound 3 | ||||||
![]() | UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase | ||||||
![]() | TRANSFERASE / lps synthesis | ||||||
Function / homology | ![]() UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase activity / UDP-3-O-(3-hydroxyacyl)glucosamine N-acyltransferase / N-acyltransferase activity / lipid A biosynthetic process / response to antibiotic / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ma, X. / Shia, S. | ||||||
![]() | ![]() Title: Structural and Biological Basis of Small Molecule Inhibition ofEscherichia coliLpxD Acyltransferase Essential for Lipopolysaccharide Biosynthesis. Authors: Ma, X. / Prathapam, R. / Wartchow, C. / Chie-Leon, B. / Ho, C.M. / De Vicente, J. / Han, W. / Li, M. / Lu, Y. / Ramurthy, S. / Shia, S. / Steffek, M. / Uehara, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 420.8 KB | Display | ![]() |
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PDB format | ![]() | 344.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.5 KB | Display | ![]() |
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Full document | ![]() | 459.2 KB | Display | |
Data in XML | ![]() | 2.1 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6p83C ![]() 6p84C ![]() 6p86C ![]() 6p87C ![]() 6p88C ![]() 6p89C ![]() 6p8aC ![]() 6p8bC ![]() 3eh0S 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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Components
#1: Protein | Mass: 36101.305 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: lpxD, lpxD_1, lpxD_2, A8C65_17800, A9R57_04450, AC789_1c01770, ACN002_0184, ACN77_17005, ACN81_28485, ACU57_18525, ACU90_26495, AM270_18210, AML07_22885, AML35_22825, APZ14_11060, AUQ13_07450, ...Gene: lpxD, lpxD_1, lpxD_2, A8C65_17800, A9R57_04450, AC789_1c01770, ACN002_0184, ACN77_17005, ACN81_28485, ACU57_18525, ACU90_26495, AM270_18210, AML07_22885, AML35_22825, APZ14_11060, AUQ13_07450, AUS26_23195, AW059_09890, AW106_08805, B1K96_12940, B7C53_01310, BANRA_00558, BANRA_00653, BANRA_02262, BANRA_03350, BET08_19125, BHF46_07835, BHS81_00700, BHS87_00855, BIZ41_19025, BJJ90_21310, BK292_13720, BK400_03560, BMT53_09465, BN17_46021, BTQ06_06540, BUE81_01655, BVL39_02135, BW690_02415, BZL31_14885, C2U48_09555, C4J69_03380, C5N07_08630, C5P01_08975, C5P43_07335, C6669_04195, C6986_01145, C7235_20180, C7B06_05915, C7B07_04225, CA593_02815, CG691_14440, CG692_09445, CG705_12975, CG706_12690, COD30_14715, COD46_06685, CR538_20590, CR539_04985, CRM83_15040, CXB56_23080, D0X26_09365, D2184_08545, D2185_20180, D2F89_01460, D3821_06260, D3O91_03240, D3Y67_16455, D9D20_18680, D9D55_03030, D9D69_06830, D9E22_13300, D9E35_14480, D9G42_07535, D9H66_18155, D9H68_13825, D9I18_15010, D9I87_01590, D9I97_03755, D9J11_16875, D9J44_14030, DIV22_06320, DL545_20340, DMZ31_06810, DNQ41_04690, DNQ45_10065, DQF57_05615, DQO13_06200, DS732_05825, DTL43_05870, EAI42_08350, EAI46_03595, EAI52_11055, EC1094V2_3672, EC3234A_2c01610, EC3426_00931, EC382_03005, ECTO6_03883, ED287_04550, ED600_04595, EEP23_00115, EFV01_09910, EFV02_20465, EFV04_15215, EFV08_17150, EFV11_08135, EFV12_18845, EFV15_17225, EFV17_09875, EIA13_13600, EL75_3585, EL79_3695, EL80_3642, ERS085374_03841, ERS150873_01122, ERS150876_00054, FORC28_5013, HW43_04650, JD73_13090, NCTC10429_04183, NCTC10865_05054, NCTC11022_04906, NCTC11126_03647, NCTC13462_02218, NCTC8500_04533, NCTC8960_01551, NCTC9037_04178, NCTC9045_04699, NCTC9055_00956, NCTC9058_02808, NCTC9062_04225, NCTC9706_01326, NCTC9969_04255, PU06_22990, RG28_03860, RK56_027945, RX35_04913, SAMEA3472043_02537, SAMEA3472044_04146, SAMEA3472047_02509, SAMEA3472070_02384, SAMEA3472080_03763, SAMEA3472114_03609, SAMEA3484427_01386, SAMEA3484429_01095, SAMEA3752553_02884, SAMEA3752557_00885, SAMEA3752559_03701, SAMEA3753064_03381, SAMEA3753097_03916, SAMEA3753290_00404, SAMEA3753300_01852, SK85_00179, WQ89_09605, WR15_02380 Plasmid: pET24a / Production host: ![]() ![]() References: UniProt: Q0P6M7, UniProt: P21645*PLUS, UDP-3-O-(3-hydroxyacyl)glucosamine N-acyltransferase #2: Chemical | #3: Chemical | ChemComp-O4V / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.84 % / Mosaicity: 0.16 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Mg formate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2014 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→79.59 Å / Num. obs: 96767 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.025 / Rrim(I) all: 0.071 / Net I/σ(I): 16.3 / Num. measured all: 705211 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3EH0 Resolution: 1.9→42.83 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.82 Å2 / Biso mean: 35.734 Å2 / Biso min: 18.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→42.83 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Origin x: -21.2578 Å / Origin y: 41.9696 Å / Origin z: 16.1342 Å
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Refinement TLS group |
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