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Yorodumi- PDB-4gl0: Putative spermidine/putrescine ABC transporter from Listeria mono... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gl0 | ||||||
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Title | Putative spermidine/putrescine ABC transporter from Listeria monocytogenes | ||||||
Components | Lmo0810 protein | ||||||
Keywords | TRANSPORT PROTEIN / structural genomics / IDP05673 / spermidine / putrescine / ABC transporter / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information polyamine binding / polyamine transport / membrane => GO:0016020 / periplasmic space Similarity search - Function | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å | ||||||
Authors | Osipiuk, J. / Zhou, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Putative spermidine/putrescine ABC transporter from Listeria monocytogenes Authors: Osipiuk, J. / Zhou, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gl0.cif.gz | 149 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gl0.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gl0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/4gl0 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/4gl0 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38590.035 Da / Num. of mol.: 1 / Fragment: UNP Residues 28-357 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: lmo0810 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y8T4 |
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-Non-polymers , 5 types, 178 molecules
#2: Chemical | ChemComp-PGE / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-EDO / #6: 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: 2.17 Å3/Da / Density % sol: 43.21 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2 M sodium chloride, 0.2 M phosphate buffer, 50% PEG-200, chymotrypsin, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 19, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.92→47.1 Å / Num. all: 26657 / Num. obs: 26657 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.099 / Χ2: 3.373 / Net I/σ(I): 13.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.92→47.1 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.26 / SU B: 5.751 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 95.09 Å2 / Biso mean: 34.6928 Å2 / Biso min: 16.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→47.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.969 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 34.2155 Å / Origin y: 2.0659 Å / Origin z: 14.313 Å
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