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Yorodumi- PDB-2xcu: Membrane-embedded monofunctional glycosyltransferase WaaA of Aqui... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xcu | ||||||
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Title | Membrane-embedded monofunctional glycosyltransferase WaaA of Aquifex aeolicus, complex with CMP | ||||||
Components | 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE | ||||||
Keywords | TRANSFERASE / KDTA / GSEA / GLYCOSYLTRANSFERASE SUPERFAMILY B / GT-B | ||||||
Function / homology | Function and homology information lipid IVA 3-deoxy-D-manno-octulosonic acid transferase / Kdo transferase activity / lipopolysaccharide core region biosynthetic process / lipid A biosynthetic process / transferase activity / plasma membrane Similarity search - Function | ||||||
Biological species | AQUIFEX AEOLICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||
Authors | Schmidt, H. / Hansen, G. / Hilgenfeld, R. / Mamat, U. / Mesters, J.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural and Mechanistic Analysis of the Membrane-Embedded Glycosyltransferase Waaa Required for Lipopolysaccharide Synthesis. Authors: Schmidt, H. / Hansen, G. / Singh, S. / Hanuszkiewicz, A. / Lindner, B. / Fukase, K. / Woodard, R.W. / Holst, O. / Hilgenfeld, R. / Mamat, U. / Mesters, J.R. #1: Journal: J.Biol.Chem. / Year: 2009 Title: Waaa of the Hyperthermophilic Bacterium Aquifex Aeolicus is a Monofunctional 3-Deoxy-D-Manno-Oct-2- Ulosonic Acid Transferase Involved in Lipopolysaccharide Biosynthesis. Authors: Mamat, U. / Schmidt, H. / Munoz, E. / Lindner, B. / Fukase, K. / Hanuszkiewicz, A. / Wu, J. / Meredith, T.C. / Woodard, R.W. / Hilgenfeld, R. / Mesters, J.R. / Holst, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xcu.cif.gz | 575 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xcu.ent.gz | 474.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xcu_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 2xcu_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2xcu_validation.xml.gz | 55.2 KB | Display | |
Data in CIF | 2xcu_validation.cif.gz | 72.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/2xcu ftp://data.pdbj.org/pub/pdb/validation_reports/xc/2xcu | HTTPS FTP |
-Related structure data
Related structure data | 2xciSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 1 - 352 / Label seq-ID: 22 - 373
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 43278.785 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Strain: AQ_326 / Plasmid: PUM216 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): SI-216 / References: UniProt: O66663 |
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-Non-polymers , 6 types, 135 molecules
#2: Chemical | ChemComp-C5P / #3: Chemical | ChemComp-1PE / #4: Chemical | ChemComp-CIT / #5: Chemical | ChemComp-BME / #6: Chemical | ChemComp-CL / | #7: 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: 2.52 Å3/Da / Density % sol: 51.27 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: HANGING-DROP VAPOR-DIFFUSION TECHNIQUE MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (10-15 MG/ML, 25 MM TRIS-HCL, PH 8.7, 0.1 M NACL, 10% GLYCEROL, 2 MM CYMAL-6, 5 MM 2-MERCAPTOETHANOL) AND ...Details: HANGING-DROP VAPOR-DIFFUSION TECHNIQUE MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (10-15 MG/ML, 25 MM TRIS-HCL, PH 8.7, 0.1 M NACL, 10% GLYCEROL, 2 MM CYMAL-6, 5 MM 2-MERCAPTOETHANOL) AND RESERVOIR (100 MM TRIS-HCL, PH 8.5, 35-40% (V/V) PEG 400, 200 MM NA-CITRATE, 50 MM 2-MERCAPTOETHANOL); SOAKING CRYSTALS IN 100 MM TRIS-HCL (PH 8.5), 36% (V/V) PEG 400, 200 MM NA-CITRATE AND 10 MM CMP FOR FOUR DAYS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: Jan 23, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0379 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→31.85 Å / Num. obs: 62789 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 47.57 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.42→2.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 6.8 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XCI Resolution: 2.42→31.22 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 17.569 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.493 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.993 Å2
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Refinement step | Cycle: LAST / Resolution: 2.42→31.22 Å
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Refine LS restraints |
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