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Yorodumi- PDB-5wi5: 2.0 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wi5 | ||||||
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Title | 2.0 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium. | ||||||
Components | UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1 | ||||||
Keywords | TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid / (2R)-2-(phosphonooxy)propanoic acid / Magnesium | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / cell cycle / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / cytoplasm Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae serotype 4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 2.0 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric ...Title: 2.0 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium. Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wi5.cif.gz | 347.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wi5.ent.gz | 279.5 KB | Display | PDB format |
PDBx/mmJSON format | 5wi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wi5_validation.pdf.gz | 4.6 MB | Display | wwPDB validaton report |
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Full document | 5wi5_full_validation.pdf.gz | 4.7 MB | Display | |
Data in XML | 5wi5_validation.xml.gz | 67.5 KB | Display | |
Data in CIF | 5wi5_validation.cif.gz | 94.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/5wi5 ftp://data.pdbj.org/pub/pdb/validation_reports/wi/5wi5 | HTTPS FTP |
-Related structure data
Related structure data | 3sg1S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 46194.023 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria) Strain: ATCC BAA-334 / TIGR4 / Gene: murA1, murA, SP_1966 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic References: UniProt: Q97NQ4, UDP-N-acetylglucosamine 1-carboxyvinyltransferase #2: Chemical | ChemComp-0V5 / ( #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-EPU / #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: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein: 8.2 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (B4), 0.01M MIB buffer (pH 7.0), 25% (w/v) PEG 1500. |
-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: Jul 12, 2017 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 113220 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.04 / Rsym value: 0.076 / Χ2: 1.008 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 5600 / CC1/2: 0.697 / Rpim(I) all: 0.405 / Rsym value: 0.756 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SG1 Resolution: 2→29.29 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.668 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.194 / 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: 50.996 Å2
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Refinement step | Cycle: 1 / Resolution: 2→29.29 Å
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Refine LS restraints |
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