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Yorodumi- PDB-4b61: In meso structure of alginate transporter, AlgE, from Pseudomoas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b61 | ||||||
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Title | In meso structure of alginate transporter, AlgE, from Pseudomoas aeruginosa, PAO1. Crystal form 3. | ||||||
Components | ALGINATE PRODUCTION PROTEIN ALGE | ||||||
Keywords | MEMBRANE PROTEIN / OUTER MEMBRANE / IN MESO CRYSTALLISATION / LIPIDIC CUBIC PHASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOMONAS AERUGINOSA PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å | ||||||
Authors | Tan, J. / Pye, V.E. / Aragao, D. / Caffrey, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: A Conformational Landscape for Alginate Secretion Across the Outer Membrane of Pseudomonas Aeruginosa. Authors: Tan, J. / Rouse, S.L. / Li, D. / Pye, V.E. / Vogeley, L. / Brinth, A.R. / El Arnaout, T. / Whitney, J.C. / Howell, P.L. / Sansom, M.S.P. / Caffrey, M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b61.cif.gz | 374.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b61.ent.gz | 307 KB | Display | PDB format |
PDBx/mmJSON format | 4b61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b61_validation.pdf.gz | 4.2 MB | Display | wwPDB validaton report |
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Full document | 4b61_full_validation.pdf.gz | 4.2 MB | Display | |
Data in XML | 4b61_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 4b61_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/4b61 ftp://data.pdbj.org/pub/pdb/validation_reports/b6/4b61 | HTTPS FTP |
-Related structure data
Related structure data | 4afkC 4azlC 3rbhS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9796, 0.1544, -0.1289), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 51199.520 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-490 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Description: HOLLOWAY COLLECTION / Plasmid: ALGE-PET200/D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P18895 |
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-Non-polymers , 7 types, 235 molecules
#2: Chemical | ChemComp-78M / ( #3: Chemical | ChemComp-LDA / | #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-CU / #6: Chemical | #7: Chemical | ChemComp-ACT / | #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE (78M): BOTH 2S AND 2R PRESENT. LIPIDS WITHOUT ...(2S)-2,3-DIHYDROXYP |
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Sequence details | STRUCTURE CONTAINS FOLLOWING RESIDUES 38-105, 117-471, 475- 490 DATABASE PSEUDOMONAS GENOME ...STRUCTURE CONTAINS FOLLOWING RESIDUES 38-105, 117-471, 475- 490 DATABASE PSEUDOMONA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.26 % / Description: NONE |
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Crystal grow | Method: lipidic cubic phase / pH: 6.5 Details: 0.1 M SODIUM CACODYLATE, PH 6.5, 1.1 M SODIUM ACETATE IN SOLUTION; PROTEIN RECONSTITUTED IN LIPIDIC CUBIC PHASE USING 7.8 MAG AS THE HOSTING LIPID. |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 17, 2009 |
Radiation | Monochromator: DOUBLE CRYSTAL CRYO-COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→55.64 Å / Num. obs: 45680 / % possible obs: 98.6 % / Observed criterion σ(I): 1.8 / Redundancy: 9.3 % / Biso Wilson estimate: 35.72 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RBH Resolution: 2.402→48.865 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 24.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.62 Å2 / ksol: 0.351 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2.402→48.865 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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