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Open data
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Basic information
Entry | Database: PDB / ID: 3kqa | ||||||
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Title | MurA dead-end complex with terreic acid | ||||||
![]() | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Open enzyme state / inside-out alpha/beta barrel / Cell cycle / Cell division / Cell shape / Cell wall biogenesis/degradation / Peptidoglycan synthesis / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Schonbrunn, E. | ||||||
![]() | ![]() Title: The fungal product terreic acid is a covalent inhibitor of the bacterial cell wall biosynthetic enzyme UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA) . Authors: Han, H. / Yang, Y. / Olesen, S.H. / Becker, A. / Betzi, S. / Schonbrunn, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 328 KB | Display | ![]() |
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PDB format | ![]() | 267.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.1 KB | Display | ![]() |
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Full document | ![]() | 503 KB | Display | |
Data in XML | ![]() | 64.7 KB | Display | |
Data in CIF | ![]() | 89.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3kr6C ![]() 3lthC ![]() 1ejcS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 44829.406 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase #2: Chemical | ChemComp-TR9 / ( #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Nonpolymer details | THE UNBOUND FROM OF THE INHIBITOR TR9 IS TERREIC ACID. UPON REACTION WITH PROTEIN IT BINDS ...THE UNBOUND FROM OF THE INHIBITOR TR9 IS TERREIC ACID. UPON REACTION WITH PROTEIN IT BINDS COVALENTLY | Sequence details | ASP67 FORMS AN ISOPEPTIDI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.96 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM CaCl2, 100 mM HEPES, pH 7.5, 30% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 15, 2009 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→15 Å / Num. all: 88863 / Num. obs: 88863 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.25→2.3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 7.9 / Num. unique all: 5612 / Rsym value: 0.079 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EJC Resolution: 2.25→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→15 Å
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.023
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