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Yorodumi- PDB-4g4v: Crystal structure of peptidoglycan-associated lipoprotein from Ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g4v | |||||||||
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Title | Crystal structure of peptidoglycan-associated lipoprotein from Acinetobacter baumannii | |||||||||
Components | Peptidoglycan-associated lipoprotein | |||||||||
Keywords | PEPTIDE BINDING PROTEIN / OmpA-like domain / MEMBRANE PROTEIN | |||||||||
Function / homology | OmpA-like domain / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / 2,6-DIAMINOPIMELIC ACID / Peptidoglycan-associated lipoprotein / Peptidoglycan-associated lipoprotein Function and homology information | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Lee, W.C. / Song, J.H. / Park, J.S. / Kim, H.Y. | |||||||||
Citation | Journal: To be Published Title: Enantiomer-dependent amino acid binding affinity of OmpA-like domains from Acinetobacter baumannii peptidoglycan-associated lipoprotein and OmpA Authors: Lee, W.C. / Park, J.S. / Song, J.H. / Kim, S.I. / Lee, J.C. / Cheong, J. / Kim, H.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g4v.cif.gz | 37.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g4v.ent.gz | 23.7 KB | Display | PDB format |
PDBx/mmJSON format | 4g4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g4v_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
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Full document | 4g4v_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 4g4v_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 4g4v_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/4g4v ftp://data.pdbj.org/pub/pdb/validation_reports/g4/4g4v | HTTPS FTP |
-Related structure data
Related structure data | 4g4wC 4g4xC 4g4yC 4g4zC 4g88C 3td4S C: citing same article (ref.) 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: 12814.040 Da / Num. of mol.: 1 / Fragment: UNP residues 75-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: TCDC-AB0715 / Gene: pal / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F0QP95, UniProt: A0A7U3YVT1*PLUS |
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#2: Chemical | ChemComp-API / |
#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: 1.85 Å3/Da / Density % sol: 33.63 % / Mosaicity: 1.278 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.2 Details: 0.1M PHOSPHATE CITRATE, 30% PEG 3350, pH 4.2, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 3, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 7884 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.071 / Χ2: 3.123 / Net I/σ(I): 16.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TD4 Resolution: 1.9→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 39.427 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.46 Å2 / Biso mean: 33.1362 Å2 / Biso min: 17.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Xplor file |
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