+Open data
-Basic information
Entry | Database: PDB / ID: 2iu9 | ||||||
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Title | Chlamydia trachomatis LpxD with 100mM UDPGlcNAc (Complex II) | ||||||
Components | UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / UDP-3- O-ACYL-GLUCOSAMINE N-ACYLTRANSFERASE / ACYLTRANSFERASE / LIPID A BIOSYNTHESIS / LEFT-HANDED BETA HELIX / COMPLEX WITH UDPGLCNAC / ENZYME / HOMOTRIMER / LIPID SYNTHESIS | ||||||
Function / homology | Function and homology information UDP-3-O-(3-hydroxyacyl)glucosamine N-acyltransferase / N-acyltransferase activity / lipid A biosynthetic process Similarity search - Function | ||||||
Biological species | CHLAMYDIA TRACHOMATIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Buetow, L. / Smith, T.K. / Dawson, A. / Fyffe, S. / Hunter, W.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: Structure and Reactivity of Lpxd, the N-Acyltransferase of Lipid a Biosynthesis Authors: Buetow, L. / Smith, T.K. / Dawson, A. / Fyffe, S. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iu9.cif.gz | 212.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iu9.ent.gz | 168.8 KB | Display | PDB format |
PDBx/mmJSON format | 2iu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iu9_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2iu9_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2iu9_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 2iu9_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/2iu9 ftp://data.pdbj.org/pub/pdb/validation_reports/iu/2iu9 | HTTPS FTP |
-Related structure data
Related structure data | 2iu8SC 2iuaC 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 40629.332 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CHLAMYDIA TRACHOMATIS (bacteria) / Variant: SEROVAR B / Plasmid: PET 15B (NOVAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O84245, UniProt: P0CD76*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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-Non-polymers , 5 types, 111 molecules
#2: Chemical | ChemComp-BME / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.5 % |
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Crystal grow | pH: 6.5 Details: PROTEIN INCUBATED WITH 100MM UDPGLCNAC AND CRYSTALLIZED FROM 1.2M AMMONIUM SULFATE, 0.1M MES, PH 6.5, 2% DIOXANE, 1MM TCEP, AND 2MM UDPGLCNAC. |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Aug 25, 2004 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→28.5 Å / Num. obs: 26254 / % possible obs: 98.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 3.1→3.19 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IU8 Resolution: 3.1→28.5 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.89 / SU B: 46.63 / SU ML: 0.407 / Cross valid method: THROUGHOUT / ESU R Free: 0.513 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.21 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→28.5 Å
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Refine LS restraints |
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