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Yorodumi- PDB-2wpq: Salmonella enterica SadA 479-519 fused to GCN4 adaptors (SadAK3, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wpq | ||||||
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Title | Salmonella enterica SadA 479-519 fused to GCN4 adaptors (SadAK3, in- register fusion) | ||||||
Components | TRIMERIC AUTOTRANSPORTER ADHESIN FRAGMENT | ||||||
Keywords | MEMBRANE PROTEIN / HYDROPHOBIC CORE / ION COORDINATION / PROTEIN EXPORT / TRIMERIC AUTOTRANSPORTER ADHESIN / TAA / POLAR CORE RESIDUES | ||||||
Function / homology | Function and homology information | ||||||
Biological species | SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Hartmann, M.D. / Hernandez Alvarez, B. / Albrecht, R. / Zeth, K. / Lupas, A.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: A Coiled-Coil Motif that Sequesters Ions to the Hydrophobic Core. Authors: Hartmann, M.D. / Ridderbusch, O. / Zeth, K. / Albrecht, R. / Testa, O. / Woolfson, D.N. / Sauer, G. / Dunin-Horkawicz, S. / Lupas, A.N. / Alvarez, B.H. #1: Journal: Protein Eng.Des.Sel. / Year: 2008 Title: A New Expression System for Protein Crystallization Using Trimeric Coiled-Coil Adaptors. Authors: Hernandez Alvarez, B. / Hartmann, M.D. / Albrecht, R. / Lupas, A.N. / Zeth, K. / Linke, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wpq.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wpq.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wpq_validation.pdf.gz | 451.3 KB | Display | wwPDB validaton report |
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Full document | 2wpq_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | 2wpq_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 2wpq_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/2wpq ftp://data.pdbj.org/pub/pdb/validation_reports/wp/2wpq | HTTPS FTP |
-Related structure data
Related structure data | 2wprC 2wpsC 2wpyC 2wpzC 2wq0C 2wq1C 2wq2C 2wq3C 1gcmS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 6 / Auth seq-ID: 450 - 548 / Label seq-ID: 1 - 99
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-Components
#1: Protein | Mass: 11532.017 Da / Num. of mol.: 3 / Fragment: RESIDUES 479-519 FUSED TO GCN4 ADAPTORS Source method: isolated from a genetically manipulated source Details: N- AND C-TERMINAL IN-REGISTER FUSION TO GCN4 ADAPTORS Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8ZL64 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | Details: 20% (W/V) PEG 3350, 0.2 M KNO3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.969 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→34 Å / Num. obs: 29718 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.97 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.85→1.96 Å / Redundancy: 3.82 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.91 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GCM Resolution: 1.85→34.14 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.891 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RECORD CONTAINS RESIDUAL B FACTORS ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.788 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→34.14 Å
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Refine LS restraints |
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