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Yorodumi- PDB-2w0w: Crystal structure of Glmu from Haemophilus influenzae in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w0w | ||||||
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Title | Crystal structure of Glmu from Haemophilus influenzae in complex with quinazoline inhibitor 2 | ||||||
Components | GLUCOSAMINE-1-PHOSPHATE N-ACETYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / PEPTIDOGLYCAN SYNTHESIS / GLMU / BACTERIAL / INHIBITOR / MAGNESIUM / CELL SHAPE / ACTIVE SITE / METAL-BINDING / CELL WALL BIOGENESIS/DEGRADATION / MULTIFUNCTIONAL ENZYME / NUCLEOTIDYLTRANSFERASE / ACYLTRANSFERASE / URIDYLTRANSFERASE | ||||||
Function / homology | Function and homology information glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / cell morphogenesis / regulation of cell shape ...glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / cell morphogenesis / regulation of cell shape / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | HAEMOPHILUS INFLUENZAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Mochalkin, I. / Melnick, M. | ||||||
Citation | Journal: To be Published Title: Discovery and Initial Sar of Quinazoline Inhibitors of Glmu from Haemophilus Influenzae Authors: Melnick, M. / Mochalkin, I. / Lightle, S. / Narasimhan, L. / Mcdowell, L. / Sarver, R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w0w.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w0w.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 2w0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w0w_validation.pdf.gz | 710.7 KB | Display | wwPDB validaton report |
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Full document | 2w0w_full_validation.pdf.gz | 715.9 KB | Display | |
Data in XML | 2w0w_validation.xml.gz | 18 KB | Display | |
Data in CIF | 2w0w_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/2w0w ftp://data.pdbj.org/pub/pdb/validation_reports/w0/2w0w | HTTPS FTP |
-Related structure data
Related structure data | 2w0vC 2v0hS 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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-Components
#1: Protein | Mass: 49346.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P43889, glucosamine-1-phosphate N-acetyltransferase |
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#2: Chemical | ChemComp-LZS / |
#3: Chemical | ChemComp-PG4 / |
#4: 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: 4 Å3/Da / Density % sol: 69 % / Description: NONE |
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Crystal grow | Details: 1.7 M AMMONIUM SULFATE, 2% PEG 400, 0.1M MES PH 5.4-6.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 24797 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 10.63 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 27.41 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.95 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V0H Resolution: 2.59→117.04 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.884 / SU B: 17.904 / SU ML: 0.201 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→117.04 Å
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Refine LS restraints |
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