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Open data
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Basic information
Entry | Database: PDB / ID: 2go4 | ||||||
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Title | Crystal structure of Aquifex aeolicus LpxC complexed with TU-514 | ||||||
![]() | UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase | ||||||
![]() | HYDROLASE / LpxC-inhibitor complex | ||||||
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. / Li, X. / Fierke, C.A. / Christianson, D.W. | ||||||
![]() | ![]() Title: Mechanistic Inferences from the Binding of Ligands to LpxC, a Metal-Dependent Deacetylase Authors: Gennadios, H.A. / Whittington, D.A. / Li, X. / Fierke, C.A. / Christianson, D.W. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ALTHOUGH IN THE CRYSTAL THIS MOLECULE APPEARS TO FORM A DIMER, THE MONOMER IS BIOLOGICALLY ACTIVE. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). | ||||||
Remark 999 | SEQUENCE THE RESIDUE NUMBERING SCHEME FOR THIS STRUCTURE FOLLOWS THAT OF THE E. COLI ENZYME. THIS ...SEQUENCE THE RESIDUE NUMBERING SCHEME FOR THIS STRUCTURE FOLLOWS THAT OF THE E. COLI ENZYME. THIS TREATMENT RESULTS IN A BREAK IN THE SEQUENTIAL NUMBERING IN A COUPLE OF PLACES. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.1 KB | Display | ![]() |
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PDB format | ![]() | 95 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 758.2 KB | Display | ![]() |
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Full document | ![]() | 770.3 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2go3C ![]() 1p42S 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | Biological monomer, however, crystallographic dimer |
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Components
#1: Protein | Mass: 30488.875 Da / Num. of mol.: 2 / Fragment: delta 11 C-terminal deletion / Mutation: 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 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.77 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES (pH 7.5), 180 mM NaCl, 14% PEG 3350, 5 mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2006 / Details: Rh coated Si monochromatic mirror |
Radiation | Monochromator: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9124 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 19244 / Num. obs: 17601 / % possible obs: 97.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Mean I/σ(I) obs: 2.2 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1P42 (zinc-inhibited LpxC) Resolution: 2.7→50 Å / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.39 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell |
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