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- PDB-2o3z: X-ray crystal structure of LpxC complexed with 3-heptyloxybenzoate -
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Open data
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Basic information
Entry | Database: PDB / ID: 2o3z | ||||||
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Title | X-ray crystal structure of LpxC complexed with 3-heptyloxybenzoate | ||||||
![]() | UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase | ||||||
![]() | HYDROLASE / Lipid A biosynthesis / Lipid synthesis / LpxC / 3-heptyloxybenzoate | ||||||
Function / homology | ![]() UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gennadios, H.A. / Whittington, D.A. / Christianson, D.W. | ||||||
![]() | ![]() Title: Amphipathic benzoic acid derivatives: synthesis and binding in the hydrophobic tunnel of the zinc deacetylase LpxC. Authors: Shin, H. / Gennadios, H.A. / Whittington, D.A. / Christianson, D.W. | ||||||
History |
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Remark 999 | SEQUENCE THE RESIDUE NUMBERING SYSTEM FOLLOWS THAT OF THE E.COLI ENZYME, AND RESULTS IN A BREAKS IN ...SEQUENCE THE RESIDUE NUMBERING SYSTEM FOLLOWS THAT OF THE E.COLI ENZYME, AND RESULTS IN A BREAKS IN THE SEQUENTIAL NUMBERING IN FEW REGIONS |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.7 KB | Display | ![]() |
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PDB format | ![]() | 97.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.1 KB | Display | ![]() |
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Full document | ![]() | 471.5 KB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p42S S: Starting model for refinement |
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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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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | There are 2 monomers in the asymmetric unit forming a crystallograpic dimer. The second monomer is generated by: X,Y,Z Y,X-Y,1/3+Z -X+Y,-X,2/3+Z -X,-Y,1/2+Z Y,-X+Y,5/6+Z X-Y,X,1/6+Z |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30989.510 Da / Num. of mol.: 2 / Mutation: deltaD284-L294, C193A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O67648, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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-Non-polymers , 5 types, 178 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/AI7.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/AI7.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.79 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM HEPES pH 7.0, 12-14% PEG3350, 180mM NaCl, 0.5mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2005 Details: sagital focusing monochromator and vertical focusing mirror |
Radiation | Monochromator: Rosenbaum-Rock double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 33203 / % possible obs: 98.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 24.6 Å2 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.25→2.28 Å / % possible obs: 99.8 % / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.5 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1P42 Resolution: 2.25→46.7 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.21 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→46.7 Å
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Refine LS restraints |
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LS refinement shell |
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