+Open data
-Basic information
Entry | Database: PDB / ID: 1q3g | ||||||
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Title | MurA (Asp305Ala) liganded with tetrahedral reaction intermediate | ||||||
Components | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
Keywords | TRANSFERASE / inside-out alpha-beta barrel | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / cytoplasm Similarity search - Function | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Eschenburg, S. / Kabsch, W. / Healy, M.L. / Schonbrunn, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: A New View of the Mechanisms of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) and 5-Enolpyruvylshikimate-3-phosphate Synthase (AroA) Derived from X-ray Structures of Their Tetrahedral ...Title: A New View of the Mechanisms of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) and 5-Enolpyruvylshikimate-3-phosphate Synthase (AroA) Derived from X-ray Structures of Their Tetrahedral Reaction Intermediate States. Authors: Eschenburg, S. / Kabsch, W. / Healy, M.L. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q3g.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1q3g.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 1q3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q3g_validation.pdf.gz | 5.4 MB | Display | wwPDB validaton report |
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Full document | 1q3g_full_validation.pdf.gz | 5.6 MB | Display | |
Data in XML | 1q3g_validation.xml.gz | 263.8 KB | Display | |
Data in CIF | 1q3g_validation.cif.gz | 334.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/1q3g ftp://data.pdbj.org/pub/pdb/validation_reports/q3/1q3g | HTTPS FTP |
-Related structure data
Related structure data | 1q36C 1a2nS 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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-Components
#1: Protein | Mass: 44785.398 Da / Num. of mol.: 16 / Mutation: N67D,D305A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: MURA / Plasmid: pET9d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase #2: Chemical | ChemComp-UDA / #3: Chemical | ChemComp-EDO / #4: 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: 2.31 Å3/Da / Density % sol: 46.74 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 20,000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→20 Å / Num. all: 185835 / Num. obs: 185835 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.3 / Num. unique all: 9008 / % possible all: 95.9 |
Reflection | *PLUS Num. obs: 809759 / % possible obs: 98.9 % |
Reflection shell | *PLUS Lowest resolution: 2.7 Å / % possible obs: 0.335 % / Num. unique obs: 26280 / Num. measured obs: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1A2N Resolution: 2.65→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.67 Å
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 2 % / Rfactor Rwork: 0.216 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.7 Å |