+Open data
-Basic information
Entry | Database: PDB / ID: 3kr6 | ||||||
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Title | MurA dead-end complex with fosfomycin | ||||||
Components | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
Keywords | TRANSFERASE/ANTIBIOTIC / closed enzyme state / inside-out alpha/beta barrel / Cell cycle / Cell division / Cell shape / Cell wall biogenesis/degradation / Peptidoglycan synthesis / TRANSFERASE / TRANSFERASE-ANTIBIOTIC complex | ||||||
Function / homology | Function and homology information 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 / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Schonbrunn, E. | ||||||
Citation | Journal: Biochemistry / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kr6.cif.gz | 104.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kr6.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 3kr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kr6_validation.pdf.gz | 809.5 KB | Display | wwPDB validaton report |
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Full document | 3kr6_full_validation.pdf.gz | 812.3 KB | Display | |
Data in XML | 3kr6_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 3kr6_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/3kr6 ftp://data.pdbj.org/pub/pdb/validation_reports/kr/3kr6 | HTTPS FTP |
-Related structure data
Related structure data | 3kqaC 3lthC 1rywS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 44872.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3189, JW3156, murA, MurA (MurZ), murZ / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P0A749, UDP-N-acetylglucosamine 1-carboxyvinyltransferase |
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#2: Chemical | ChemComp-FFQ / [( |
#3: Chemical | ChemComp-UD1 / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | THE UNBOUND FORM OF THE ANTIBIOTIC IS FOSFOMYCIN. UPON REACTION WITH PROTEIN, IT COVALENTLY BINDS ...THE UNBOUND FORM OF THE ANTIBIOTIC |
Sequence details | ASP67 FORMS AN ISOPEPTIDI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12.5 mM Na-formate, 25 mM Na/K phosphate, 10% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 7, 2008 / 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: 1.7→20 Å / Num. all: 59154 / Num. obs: 59154 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 15.2 / Num. unique all: 8874 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RYW Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 17.1 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.015
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