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- PDB-1kfm: Core side-chain packing and backbone conformation in Lpp-56 coile... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kfm | ||||||
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Title | Core side-chain packing and backbone conformation in Lpp-56 coiled-coil mutants | ||||||
![]() | MAJOR OUTER MEMBRANE LIPOPROTEIN | ||||||
![]() | MEMBRANE PROTEIN / LIPOPROTEIN / PROTEIN FOLDING / HELIX CAPPING / ALANINE-ZIPPER | ||||||
Function / homology | ![]() periplasmic space organization / lipid modification / peptidoglycan binding / cell outer membrane / outer membrane-bounded periplasmic space / lipid binding / extracellular region / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, J. / Cao, W. / Lu, M. | ||||||
![]() | ![]() Title: Core side-chain packing and backbone conformation in Lpp-56 coiled-coil mutants. Authors: Liu, J. / Cao, W. / Lu, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 19.8 KB | Display | ![]() |
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PDB format | ![]() | 12.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 359.7 KB | Display | ![]() |
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Full document | ![]() | 361.1 KB | Display | |
Data in XML | ![]() | 2.2 KB | Display | |
Data in CIF | ![]() | 2.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kfnC ![]() 1eq7S ![]() 1jcb S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The biological assembly is a trimer generated from the monomer by the three fold axis. |
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Components
#1: Protein | Mass: 6073.553 Da / Num. of mol.: 1 / Mutation: M30A, V34A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.98 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 4000, sodium cacodylate, ammonium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP at 293K, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Oct 12, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 2761 / Num. obs: 2761 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 12.3 / Num. unique all: 267 / % possible all: 97 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. measured all: 20868 / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS Highest resolution: 2 Å / Rmerge(I) obs: 0.097 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EQ7 Resolution: 2→25.26 Å / Rfactor Rfree error: 0.018 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.1498 Å2 / ksol: 0.425897 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→25.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.074 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor obs: 0.26 / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å / Rfactor Rfree: 0.356 / Rfactor Rwork: 0.353 |