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Yorodumi- PDB-1e8c: Structure of MurE the UDP-N-acetylmuramyl tripeptide synthetase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e8c | |||||||||
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Title | Structure of MurE the UDP-N-acetylmuramyl tripeptide synthetase from E. coli | |||||||||
Components | UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE | |||||||||
Keywords | LIGASE / PEPTIDOGLYCAN BIOSYNTHESIS | |||||||||
Function / homology | Function and homology information UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | |||||||||
Authors | Gordon, E.J. / Chantala, L. / Dideberg, O. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystal Structure of Udp-N-Acetylmuramoyl-L-Alanyl-D-Glutamate: Meso-Diaminopimelate Ligase from Escherichia Coli Authors: Gordon, E.J. / Flouret, B. / Chantalat, L. / Van Heijenoort, J. / Mengin-Lecreulx, D. / Dideberg, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e8c.cif.gz | 213.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e8c.ent.gz | 170.1 KB | Display | PDB format |
PDBx/mmJSON format | 1e8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e8c_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1e8c_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1e8c_validation.xml.gz | 44.3 KB | Display | |
Data in CIF | 1e8c_validation.cif.gz | 60.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/1e8c ftp://data.pdbj.org/pub/pdb/validation_reports/e8/1e8c | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.042, -0.999, -0.012), Vector: |
-Components
#1: Protein | Mass: 54401.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: UDP-N-ACETYLMURAMYL-TRIPEPTIDE BOUND IN ACTIVE SITE Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Gene: MURE / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P22188, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase #2: Chemical | ChemComp-CL / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | RESIDUES AFTER 494 BELONG TO LINKER AND HIS TAG USED TO EXPRESS AND PURIFY THE PROTEIN | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP EXPERIMENT RESERVOIR: 13% PEG MME 5K, 0.5M LICL, 10% ISOPROPANOL, 0.1M HEPES PH 7.5, 5MM DTT, 1MM UDP-TRIPEPTIDE DROP: 2UL PROTEIN SOLUTION (MURE @ 10MGML-1 IN 20MM HEPES PH 7. ...Details: HANGING DROP EXPERIMENT RESERVOIR: 13% PEG MME 5K, 0.5M LICL, 10% ISOPROPANOL, 0.1M HEPES PH 7.5, 5MM DTT, 1MM UDP-TRIPEPTIDE DROP: 2UL PROTEIN SOLUTION (MURE @ 10MGML-1 IN 20MM HEPES PH 7.5, 200MM NACL, 5MM DTT) WITH 2UL RESERVOIR SOLUTION. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9791,0.9790,0.8550,0.93 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 15, 1999 | |||||||||||||||
Radiation | Monochromator: GE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→46.7 Å / Num. obs: 323548 / % possible obs: 98.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.066 | |||||||||||||||
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 3.9 % / Rsym value: 0.22 / % possible all: 91.2 | |||||||||||||||
Reflection | *PLUS Num. obs: 72674 / Num. measured all: 323548 / Rmerge(I) obs: 0.066 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 91.2 % / Rmerge(I) obs: 0.22 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→46.73 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3518491.82 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.2391 Å2 / ksol: 0.318364 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→46.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.25 |