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Yorodumi- PDB-6nkj: 1.3 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nkj | ||||||
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Title | 1.3 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with (2R)-2-(phosphonooxy)propanoic acid. | ||||||
Components | UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1 | ||||||
Keywords | TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / (2R)-2-(phosphonooxy)propanoic acid | ||||||
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: 1.3 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 1.3 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with (2R)-2-(phosphonooxy)propanoic acid. Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / 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 | 6nkj.cif.gz | 392.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nkj.ent.gz | 320.7 KB | Display | PDB format |
PDBx/mmJSON format | 6nkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nkj_validation.pdf.gz | 475 KB | Display | wwPDB validaton report |
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Full document | 6nkj_full_validation.pdf.gz | 482.3 KB | Display | |
Data in XML | 6nkj_validation.xml.gz | 48.2 KB | Display | |
Data in CIF | 6nkj_validation.cif.gz | 77.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/6nkj ftp://data.pdbj.org/pub/pdb/validation_reports/nk/6nkj | 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46194.023 Da / Num. of mol.: 2 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 BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) MAGIC References: UniProt: Q97NQ4, UDP-N-acetylglucosamine 1-carboxyvinyltransferase |
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-Non-polymers , 5 types, 1329 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: 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: 3.07 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein: 11.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (B9), 1.8M Ammonium citrate pH=7.0; Cryo: 1.8M Ammonium citrate pH=7.0, 25% Sucrose. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 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: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. obs: 285243 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.029 / Rrim(I) all: 0.057 / Rsym value: 0.049 / Χ2: 1.005 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 14279 / CC1/2: 0.725 / Rpim(I) all: 0.378 / Rrim(I) all: 0.712 / Rsym value: 0.599 / Χ2: 1.005 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SG1 Resolution: 1.3→27.77 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.404 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.4 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→27.77 Å
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