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Yorodumi- PDB-2ies: Crystal Structure of Aquifex aeolicus LpxC Complexed with Pyropho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ies | ||||||
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Title | Crystal Structure of Aquifex aeolicus LpxC Complexed with Pyrophosphate | ||||||
Components | UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase | ||||||
Keywords | HYDROLASE / alpha + beta fold | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Gennadios, H.A. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Binding of Uridine 5-Diphosphate in the Basic Patch of the Zinc Metalloenzyme Deacetylase LpxC and Implications for Substrate Binding Authors: Gennadios, H.A. / Christianson, D.W. | ||||||
History |
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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 | 2ies.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ies.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ies.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ies_validation.pdf.gz | 780.3 KB | Display | wwPDB validaton report |
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Full document | 2ies_full_validation.pdf.gz | 786.7 KB | Display | |
Data in XML | 2ies_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 2ies_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/2ies ftp://data.pdbj.org/pub/pdb/validation_reports/ie/2ies | HTTPS FTP |
-Related structure data
Related structure data | 2ierC 1p42S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | This protein forms a crystallographic dimer and is not known to be a dimer in solution. The second monomer can be generated by the following symmetry operations: -y, x-y, z+1/3 and -x+y, -x, z+2/3 and -x, -y, z+1/2 and y, -x+y, z+5/6 and x-y, x, z+1/6. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30989.510 Da / Num. of mol.: 2 / Mutation: C193A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: lpxC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS References: UniProt: O67648, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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-Non-polymers , 5 types, 35 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.82 Å3/Da / Density % sol: 56.46 % |
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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, 10% PEG 3350, 0.5 mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 26, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 12560 / Redundancy: 2.65 % / Biso Wilson estimate: 39.4 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 2.65 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 2 / Num. unique all: 1260 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P42 Resolution: 3.1→50 Å / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.1→50 Å
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Refine LS restraints |
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LS refinement shell |
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