+Open data
-Basic information
Entry | Database: PDB / ID: 3v5v | ||||||
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Title | UNLIGANDED E.CLOACAE C115D MURA | ||||||
Components | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
Keywords | TRANSFERASE / MURA / OPEN ENZYME STATE / CELL WALL / BIOGENESIS/DEGRADATION / PEPTIDOGLYCAN SYNTHESIS | ||||||
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 | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Zhu, J.-Y. / Yang, Y. / Schonbrunn, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Functional Consequence of Covalent Reaction of Phosphoenolpyruvate with UDP-N-acetylglucosamine 1-Carboxyvinyltransferase (MurA). Authors: Zhu, J.Y. / Yang, Y. / Han, H. / Betzi, S. / Olesen, S.H. / Marsilio, F. / Schonbrunn, E. | ||||||
History |
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Remark 999 | IAS67 FORMS AN ISOPEPTIDIC BOND AND IS A RESULT OF POSTTRANSLATIONAL MODIFICATION OF ASN67 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v5v.cif.gz | 328.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v5v.ent.gz | 267.7 KB | Display | PDB format |
PDBx/mmJSON format | 3v5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v5v_validation.pdf.gz | 521.7 KB | Display | wwPDB validaton report |
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Full document | 3v5v_full_validation.pdf.gz | 561.5 KB | Display | |
Data in XML | 3v5v_validation.xml.gz | 70.3 KB | Display | |
Data in CIF | 3v5v_validation.cif.gz | 96 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/3v5v ftp://data.pdbj.org/pub/pdb/validation_reports/v5/3v5v | HTTPS FTP |
-Related structure data
Related structure data | 3spbC 3su9C 3swaC 3swdC 3sweC 3swgC 3swiC 3swqC 3upkC 3v4tC 1ejdS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 44841.352 Da / Num. of mol.: 4 / Mutation: C115D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_04571, murA, murZ / Plasmid: PET9D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase |
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-Non-polymers , 5 types, 516 molecules
#2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-PGE / | #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: 2.45 Å3/Da / Density % sol: 49.86 % |
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Crystal grow | Temperature: 291 K / pH: 7.5 Details: 20 MG/ML MURA C115D, 25 MM HEPES PH 7.5, 50 MM BIS-TRIS PH 5.5, 100 MM AMMONIUM ACETATE, 12.5 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 19, 2010 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 48907 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.121 / Rsym value: 0.078 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.299 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EJD Resolution: 2.7→19.89 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 4688491.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 22.22 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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