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Yorodumi- PDB-5u4h: 1.05 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u4h | ||||||
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Title | 1.05 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Acinetobacter baumannii in Covalently Bound Complex with (2R)-2-(phosphonooxy)propanoic Acid. | ||||||
Components | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
Keywords | LIPID BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Lipid-Binding Protein | ||||||
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 / cytoplasm Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 1.05 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Acinetobacter baumannii in Covalently Bound Complex with (2R)-2-(phosphonooxy)propanoic Acid. Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u4h.cif.gz | 431.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u4h.ent.gz | 353.4 KB | Display | PDB format |
PDBx/mmJSON format | 5u4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u4h_validation.pdf.gz | 458.3 KB | Display | wwPDB validaton report |
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Full document | 5u4h_full_validation.pdf.gz | 464 KB | Display | |
Data in XML | 5u4h_validation.xml.gz | 46.2 KB | Display | |
Data in CIF | 5u4h_validation.cif.gz | 74.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/5u4h ftp://data.pdbj.org/pub/pdb/validation_reports/u4/5u4h | HTTPS FTP |
-Related structure data
Related structure data | 5bq2S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44957.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: murA, A7934_11825, AA954_10900, AB895_2172, AB988_1977, ABUW_3250, ACX60_14965, APD06_13410, APD31_13720, AQ480_13100, AQ482_08180, AZE33_03430, IOMTU433_3164, IX87_17660, LV38_01284 Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic References: UniProt: A0A0R0VXX6, UDP-N-acetylglucosamine 1-carboxyvinyltransferase #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-FMT / #4: Chemical | #5: 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: 2.08 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein: 17.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3); Screen: JCSG+ (F8), 2.1M DL-Malic acid (pH 7.0); Cryo: 4M Sodium formate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2016 / Details: C(111) |
Radiation | Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→20 Å / Num. obs: 357259 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 7.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.05→1.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.919 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BQ2 Resolution: 1.05→19.96 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.963 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.965 Å2
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Refinement step | Cycle: 1 / Resolution: 1.05→19.96 Å
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