+Open data
-Basic information
Entry | Database: PDB / ID: 4m0d | ||||||
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Title | Crystal structure of MurQ from H.influenzae in apo form | ||||||
Components | N-acetylmuramic acid 6-phosphate etherase | ||||||
Keywords | LYASE / NAD(P)/FAD- binding Rossmann fold / Alpha-Beta-Alpha sandwich / MurQ / YfeU | ||||||
Function / homology | Function and homology information N-acetylmuramic acid 6-phosphate etherase / N-acetylmuramic acid catabolic process / 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process / amino sugar catabolic process / ether hydrolase activity / carbon-oxygen lyase activity / fructose-6-phosphate binding / peptidoglycan turnover / response to fructose / enzyme inhibitor activity ...N-acetylmuramic acid 6-phosphate etherase / N-acetylmuramic acid catabolic process / 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process / amino sugar catabolic process / ether hydrolase activity / carbon-oxygen lyase activity / fructose-6-phosphate binding / peptidoglycan turnover / response to fructose / enzyme inhibitor activity / glucose homeostasis / carbohydrate binding / enzyme binding / cytosol Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.577 Å | ||||||
Authors | Hazra, S. / Blanchard, J. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Structure of MurNAc 6-phosphate hydrolase (MurQ) from Haemophilus influenzae with a bound inhibitor. Authors: Hadi, T. / Hazra, S. / Tanner, M.E. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m0d.cif.gz | 227.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m0d.ent.gz | 185.3 KB | Display | PDB format |
PDBx/mmJSON format | 4m0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m0d_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
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Full document | 4m0d_full_validation.pdf.gz | 487.8 KB | Display | |
Data in XML | 4m0d_validation.xml.gz | 45.8 KB | Display | |
Data in CIF | 4m0d_validation.cif.gz | 64.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/4m0d ftp://data.pdbj.org/pub/pdb/validation_reports/m0/4m0d | HTTPS FTP |
-Related structure data
Related structure data | 4lzjC 1nriS 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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Unit cell |
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-Components
#1: Protein | Mass: 32564.734 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: Rd KW20 / Gene: murQ / Production host: Escherichia coli (E. coli) References: UniProt: P44862, N-acetylmuramic acid 6-phosphate etherase #2: 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: 2.19 Å3/Da / Density % sol: 43.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Nacl, 0.1 M Bis-Tris:HCl, pH 5.5, 25% (w/v) PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 65 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→32.56 Å / Num. all: 35231 / Num. obs: 34265 / Redundancy: 5.5 % |
Reflection shell | Highest resolution: 2.58 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NRI Resolution: 2.577→32.563 Å / SU ML: 0.42 / σ(F): 0.11 / Phase error: 30.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.577→32.563 Å
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Refine LS restraints |
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LS refinement shell |
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