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Yorodumi- PDB-1gg4: CRYSTAL STRUCTURE OF ESCHERICHIA COLI UDPMURNAC-TRIPEPTIDE D-ALAN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gg4 | ||||||
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Title | CRYSTAL STRUCTURE OF ESCHERICHIA COLI UDPMURNAC-TRIPEPTIDE D-ALANYL-D-ALANINE-ADDING ENZYME (MURF) AT 2.3 ANGSTROM RESOLUTION | ||||||
Components | UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6-DIAMINOPIMELATE-D-ALANYL-D-ALANYL LIGASE | ||||||
Keywords | LIGASE / alpha/beta sheet | ||||||
Function / homology | Function and homology information UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Yan, Y. / Munshi, S. / Chen, Z. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structure of Escherichia coli UDPMurNAc-tripeptide d-alanyl-d-alanine-adding enzyme (MurF) at 2.3 A resolution. Authors: Yan, Y. / Munshi, S. / Leiting, B. / Anderson, M.S. / Chrzas, J. / Chen, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gg4.cif.gz | 178.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gg4.ent.gz | 141.8 KB | Display | PDB format |
PDBx/mmJSON format | 1gg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gg4_validation.pdf.gz | 378.4 KB | Display | wwPDB validaton report |
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Full document | 1gg4_full_validation.pdf.gz | 402.3 KB | Display | |
Data in XML | 1gg4_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 1gg4_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/1gg4 ftp://data.pdbj.org/pub/pdb/validation_reports/gg/1gg4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47910.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET30A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11880, EC: 6.3.2.15 #2: 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: 3.56 Å3/Da / Density % sol: 65.44 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: evaporation / pH: 9.4 Details: PEG 8000, magnesium sulfate, glycerol, pH 9.4, EVAPORATION, temperature 278K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 11, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→8 Å / Num. obs: 46843 / % possible obs: 82 % / Rmerge(I) obs: 0.065 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.338 / Num. unique all: 3123 / % possible all: 54 |
Reflection | *PLUS Num. obs: 47573 / % possible obs: 82 % / Num. measured all: 545211 |
Reflection shell | *PLUS % possible obs: 54 % |
-Processing
Software |
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Refinement | Resolution: 2.3→8 Å / Cross valid method: FREE R-VALUE / Details: XPLOR
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 46843 / Rfactor Rfree: 0.282 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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