+Open data
-Basic information
Entry | Database: PDB / ID: 4cvk | ||||||||||||
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Title | PaMurF in complex with UDP-MurNAc-tripeptide (mDAP) | ||||||||||||
Components |
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Keywords | LIGASE / MURF / TRIPEPTIDE | ||||||||||||
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 / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||||||||
Authors | Ruane, K.M. / Majce, V. | ||||||||||||
Citation | Journal: To be Published Title: Pamurf in Complex with Udp-Murnac-Tripeptide (Mdap) Authors: Majce, V. / Ruane, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cvk.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cvk.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 4cvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cvk_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4cvk_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4cvk_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 4cvk_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/4cvk ftp://data.pdbj.org/pub/pdb/validation_reports/cv/4cvk | HTTPS FTP |
-Related structure data
Related structure data | 1gg4S S: Starting model for refinement |
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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: 49365.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: murF / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9HVZ7 |
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#2: Protein/peptide | Mass: 390.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-UDP / |
#4: Sugar | ChemComp-MUB / |
#5: Water | ChemComp-HOH / |
Sequence details | CONTAINS A C-TERM HIS TAG |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | Details: 0.2 M MG FORMATE, 20 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→49.04 Å / Num. obs: 36216 / % possible obs: 99.3 % / Observed criterion σ(I): 2.4 / Redundancy: 4.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.92→1.97 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GG4 Resolution: 1.92→49.04 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.766 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.304 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→49.04 Å
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Refine LS restraints |
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