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Yorodumi- PDB-2go3: Crystal structure of Aquifex aeolicus LpxC complexed with imidazole. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2go3 | ||||||
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Title | Crystal structure of Aquifex aeolicus LpxC complexed with imidazole. | ||||||
Components | UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase | ||||||
Keywords | HYDROLASE / LpxC-imidazole complex | ||||||
Function / homology | Function and homology information 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 | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Gennadios, H.A. / Whittington, D.A. / Li, X. / Fierke, C.A. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2006 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2go3.cif.gz | 135.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2go3.ent.gz | 104.1 KB | Display | PDB format |
PDBx/mmJSON format | 2go3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2go3_validation.pdf.gz | 662.6 KB | Display | wwPDB validaton report |
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Full document | 2go3_full_validation.pdf.gz | 672.8 KB | Display | |
Data in XML | 2go3_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 2go3_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/2go3 ftp://data.pdbj.org/pub/pdb/validation_reports/go/2go3 | HTTPS FTP |
-Related structure data
-Links
-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 |
-Components
-Protein , 1 types, 2 molecules AB
#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.) Aquifex aeolicus (bacteria) / Gene: lpxC, envA / Plasmid: pET21a / Production host: Escherichia coli (E. coli) References: UniProt: O67648, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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-Non-polymers , 7 types, 428 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-PLM / | #5: Chemical | #6: Chemical | ChemComp-IMD / #7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.48 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM HEPES (pH 8.0), 180 mM NaCl, 10% PEG 3350, and 5 mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 13, 2003 Details: a KOHZU double crystal monochromator with a sagittally focused second crystal. Two spherical mirrors, one will be rhodium coated. |
Radiation | Monochromator: a KOHZU double crystal monochromator with a sagittally focused second crystal. Two spherical mirrors, one will be rhodium coated. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 47793 / Num. obs: 47936 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.9 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→30 Å / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.17 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell |
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