+Open data
-Basic information
Entry | Database: PDB / ID: 4zlh | ||||||
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Title | Structure of the LapB cytoplasmic domain at 2 angstroms | ||||||
Components | Lipopolysaccharide assembly protein B | ||||||
Keywords | METAL BINDING PROTEIN / Nine TPR motifs Rubredoxin Lipopolysaccharide Regulation | ||||||
Function / homology | Function and homology information : / lipopolysaccharide metabolic process / regulation of lipid biosynthetic process / membrane => GO:0016020 / iron ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Prince, C.C. / Jia, Z. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Structure / Year: 2015 Title: An Unexpected Duo: Rubredoxin Binds Nine TPR Motifs to Form LapB, an Essential Regulator of Lipopolysaccharide Synthesis. Authors: Prince, C. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zlh.cif.gz | 145.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zlh.ent.gz | 113.4 KB | Display | PDB format |
PDBx/mmJSON format | 4zlh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/4zlh ftp://data.pdbj.org/pub/pdb/validation_reports/zl/4zlh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 38869.441 Da / Num. of mol.: 2 / Fragment: unp residues 51-389 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: lapB, yciM, Z2526, ECs1853 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AB60 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.09 % / Description: Plate clusters |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M (NH4)2SO4, 25% PEG 3350, and 0.1 M Bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.28292 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28292 Å / Relative weight: 1 |
Reflection | Resolution: 2→40.1 Å / Num. obs: 97844 / % possible obs: 99.7 % / Redundancy: 3.15 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.01 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→40.075 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 26.93 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40.075 Å
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Refine LS restraints |
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LS refinement shell |
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