+Open data
-Basic information
Entry | Database: PDB / ID: 1ejd | ||||||
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Title | Crystal structure of unliganded mura (type1) | ||||||
Components | UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / inside-out alpha/beta barrel | ||||||
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 / SYNCHROTRON / Resolution: 1.55 Å | ||||||
Authors | Eschenburg, S. / Schonbrunn, E. | ||||||
Citation | Journal: Proteins / Year: 2000 Title: Comparative X-ray analysis of the un-liganded fosfomycin-target murA. Authors: Eschenburg, S. / Schonbrunn, E. #1: Journal: Biochemistry / Year: 2000 Title: Role of the Loop Containing Residue 115 in the Induced-fit Mechanism of the Bacterial Cell Wall Biosynthetic Enzyme MurA Authors: Schonbrunn, E. / Eschenburg, S. / Krekel, F. / Luger, K. / Amrhein, N. #2: Journal: Structure / Year: 1996 Title: Crystal structure of UDP-N-acetylglucosamine enolpyruvyltransferase, the target of the antibiotic fosfomycin Authors: Schonbrunn, E. / Sack, S. / Eschenburg, S. / Perrakis, A. / Krekel, F. / Amrhein, N. / Mandelkow, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ejd.cif.gz | 196.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ejd.ent.gz | 155.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ejd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ejd_validation.pdf.gz | 473.3 KB | Display | wwPDB validaton report |
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Full document | 1ejd_full_validation.pdf.gz | 484.3 KB | Display | |
Data in XML | 1ejd_validation.xml.gz | 42.5 KB | Display | |
Data in CIF | 1ejd_validation.cif.gz | 64.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/1ejd ftp://data.pdbj.org/pub/pdb/validation_reports/ej/1ejd | HTTPS FTP |
-Related structure data
Related structure data | 1ejcC 1nawS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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5 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 44829.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-HAI / #4: 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: 3.19 Å3/Da / Density % sol: 61.45 % | ||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1 M sodium/potassium phosphate including 30 mM cyclohexylammonium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 6.4 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 6, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→17 Å / Num. all: 155426 / Num. obs: 155426 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.75 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.55→1.57 Å / Rmerge(I) obs: 0.246 / % possible all: 87.1 |
Reflection | *PLUS Num. measured all: 738470 |
Reflection shell | *PLUS % possible obs: 87.1 % / Mean I/σ(I) obs: 3.9 |
-Processing
Software |
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Refinement | Starting model: 1NAW without solvent molecules Resolution: 1.55→17 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: the following HOH were modelled as alternatives to their respective PO4: HOH 9 PO4 2424 HOH 1 PO4 2432 HOH 7 PO4 2427 HOH 11 PO4 2432 There is either the HOH molecule or the PO4, so they do ...Details: the following HOH were modelled as alternatives to their respective PO4: HOH 9 PO4 2424 HOH 1 PO4 2432 HOH 7 PO4 2427 HOH 11 PO4 2432 There is either the HOH molecule or the PO4, so they do not see each other. The PO4 ions in these HOH-PO4 pairs are labelled alternate conformation A, and the HOH is labelled alternate conformation B. The same is valid for O HOH 8 and NH2 ARG252 in chain B. The water molecule occupies one of the alternative side chain positions. HOH 8 has alternate conformation A, since it occupies alternate conformation A NH2 ARG252.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.2566 Å2 / ksol: 0.388307 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→17 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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