+Open data
-Basic information
Entry | Database: PDB / ID: 1t8z | ||||||
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Title | Atomic Structure of A Novel Tryptophan-Zipper Pentamer | ||||||
Components | Major outer membrane lipoprotein | ||||||
Keywords | MEMBRANE PROTEIN / LIPOPROTEIN / PROTEIN FOLDING / COILED COIL / PENTAMER / TRYPTOPHAN-ZIPPER | ||||||
Function / homology | Function and homology information periplasmic space organization / lipid modification / peptidoglycan binding / cell outer membrane / outer membrane-bounded periplasmic space / lipid binding / extracellular region / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å | ||||||
Authors | Liu, J. / Yong, W. / Deng, Y. / Kallenbach, N.R. / Lu, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Atomic structure of a tryptophan-zipper pentamer. Authors: Liu, J. / Yong, W. / Deng, Y. / Kallenbach, N.R. / Lu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t8z.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t8z.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 1t8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/1t8z ftp://data.pdbj.org/pub/pdb/validation_reports/t8/1t8z | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | The biological assembly is a pentamer |
-Components
#1: Protein | Mass: 6881.178 Da / Num. of mol.: 5 Mutation: I6W, L9W, V13W, L16W, V20W, L23W, V27W, M30W, V34W, A37W, A41W, A44W, L48W, M51W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: LPP, MLPA, MULI, B1677, C2072, Z2705, ECS2384, SF1706, S1839 Production host: Escherichia coli (E. coli) / References: UniProt: P69776 #2: Chemical | #3: Chemical | ChemComp-12P / | #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 Å3/Da / Density % sol: 39.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 400, Tris-HCl, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2003 |
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→70.7 Å / Num. all: 38990 / Num. obs: 38990 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.6 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.45→70.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.582 / SU ML: 0.092 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 29.899 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→70.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.452→1.49 Å / Total num. of bins used: 20 /
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