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Yorodumi- PDB-1p4n: Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-pentap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p4n | ||||||
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Title | Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-pentapeptide complex | ||||||
Components |
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Keywords | Transferase/Transferase Substrate / FemX / Transferase-Transferase Substrate complex | ||||||
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) Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / difference fourier synthesis / Resolution: 1.9 Å | ||||||
Authors | Biarrotte-Sorin, S. / Maillard, A. / 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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Remark 600 | HETEROGEN The residue FGA is gamma-glutamic acid but does not make classical peptide bond. It makes ...HETEROGEN The residue FGA is gamma-glutamic acid but does not make classical peptide bond. It makes peptide bond on the side chain at the Cgamma. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p4n.cif.gz | 96.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p4n.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 1p4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p4n_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 1p4n_full_validation.pdf.gz | 452.2 KB | Display | |
Data in XML | 1p4n_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 1p4n_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/1p4n ftp://data.pdbj.org/pub/pdb/validation_reports/p4/1p4n | HTTPS FTP |
-Related structure data
Related structure data | 1ne9SC 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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1 |
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Unit cell |
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-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: GenBank: 11999275, UniProt: Q9EY50*PLUS, UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase | ||||
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#2: Protein/peptide | Mass: 1150.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) | ||||
#3: Chemical | #4: Chemical | #5: 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: 2.23 Å3/Da / Density % sol: 44.8 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 2K, 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: 0.979711 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 14, 2002 Details: two crystals monochromator between two cylindrical parabolic mirrors |
Radiation | Monochromator: Sagitally focused Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979711 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15.57 Å / Num. obs: 27221 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 12.7 Å2 / Rsym value: 0.073 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 3947 / Rsym value: 0.19 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 102033 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.19 |
-Processing
Software |
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Refinement | Method to determine structure: difference fourier synthesis Starting model: PDB ENTRY 1NE9 Resolution: 1.9→15.57 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1090877 / Data cutoff high rms absF: 1090877 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / 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: 54.1592 Å2 / ksol: 0.39732 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→15.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2 Å |