+Open data
-Basic information
Entry | Database: PDB / ID: 4c00 | ||||||
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Title | Crystal structure of TamA from E. coli | ||||||
Components | TRANSLOCATION AND ASSEMBLY MODULE TAMA | ||||||
Keywords | TRANSPORT PROTEIN / YTFM / POLYPEPTIDE TRANSPORT-ASSOCIATED / AUTOTRANSPORTER BIOGENESIS / AUTOTRANSPORTER ASSEMBLY / OUTER MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information TAM protein secretion complex / protein localization to outer membrane / protein secretion / cell outer membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Gruss, F. / Zaehringer, F. / Jakob, R.P. / Burmann, B.M. / Hiller, S. / Maier, T. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: The Structural Basis of Autotransporter Translocation by Tama Authors: Gruss, F. / Zaehringer, F. / Jakob, R.P. / Burmann, B.M. / Hiller, S. / Maier, T. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c00.cif.gz | 359.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c00.ent.gz | 302.6 KB | Display | PDB format |
PDBx/mmJSON format | 4c00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/4c00 ftp://data.pdbj.org/pub/pdb/validation_reports/c0/4c00 | HTTPS FTP |
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-Related structure data
Related structure data | 4bzaSC 2qdz S: Starting model for refinement C: citing same article (ref.) |
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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: 62902.551 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-577 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): OMP3 / References: UniProt: P0ADE4 | ||||||||||
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#2: Chemical | ChemComp-MC3 / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE (MC3): LIPIDS IN STRUCTURE WERE BUILT AS FRAGMENTS OF ...1,2-DIMYRISTOY | Sequence details | WITHOUT N-TERMINAL SIGNAL SEQUENCE (AA. 1-21),COMPRISES AA. 22-577,ADDITIONAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.66 Å3/Da / Density % sol: 73.63 % / Description: NONE |
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Crystal grow | Details: IMIDAZOLE PH 6.0, NA ACETATE, TRIS, NACL, BETA-OG, DMPC, CHAPSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→74 Å / Num. obs: 55995 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 7.29 % / Biso Wilson estimate: 41.15 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.74 |
Reflection shell | Resolution: 2.25→2.39 Å / Redundancy: 7.04 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.39 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2QDZ AND 4BZA Resolution: 2.25→74.269 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 22.46 / Stereochemistry target values: ML Details: POTRA DOMAIN 1 AND C-TERMINUS EXHIBIT HIGHER FLEXIBILITY RESP. DISORDER. STRUCTURE OF ISOLATED POTRA DOMAINS FROM PDB 4BZA GUIDED MODEL BUILDING OF POTRA DOMAIN 1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→74.269 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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