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Yorodumi- PDB-1ne9: Crystal Structure of Weissella viridescens FemX at 1.7 Ang Resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ne9 | ||||||
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Title | Crystal Structure of Weissella viridescens FemX at 1.7 Ang Resolution | ||||||
Components | FemX | ||||||
Keywords | LIGASE / protein | ||||||
Function / homology | Function and homology information UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase / UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape Similarity search - Function | ||||||
Biological species | Weissella viridescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Biarrotte-Sorin, S. / Maillard, A.P. / Delettre, J. / Sougakoff, W. / Arthur, M. / Mayer, C. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Crystal structures of Weissella viridescens FemX and its complex with UDP-MurNAc-pentapeptide: insights into FemABX family substrates recognition. Authors: Biarrotte-Sorin, S. / Maillard, A.P. / Delettre, J. / Sougakoff, W. / Arthur, M. / Mayer, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ne9.cif.gz | 90.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ne9.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ne9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ne9_validation.pdf.gz | 427.5 KB | Display | wwPDB validaton report |
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Full document | 1ne9_full_validation.pdf.gz | 430 KB | Display | |
Data in XML | 1ne9_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 1ne9_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/1ne9 ftp://data.pdbj.org/pub/pdb/validation_reports/ne/1ne9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the biological assembly is the monomer from the asymmetric unit |
-Components
#1: Protein | Mass: 38195.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Weissella viridescens (bacteria) / Gene: femx / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9EY50 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.18 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 6K, NaCl, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: BM30A / Wavelength: 0.97976 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 14, 2002 / Details: two crystals monochromator |
Radiation | Monochromator: mirror + double crystal + mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97976 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.4 Å / Num. obs: 36921 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.044 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 3.7 / Num. unique all: 5314 / Rsym value: 0.139 / % possible all: 97.7 |
Reflection | *PLUS Lowest resolution: 35 Å / Num. measured all: 156408 / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 97.7 % / Rmerge(I) obs: 0.139 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→19.37 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.2699 Å2 / ksol: 0.430689 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.79 Å |