+Open data
-Basic information
Entry | Database: PDB / ID: 3e3c | ||||||
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Title | Structure of GrlR-lipid complex | ||||||
Components | L0044 | ||||||
Keywords | LIPID BINDING PROTEIN / GrlR / LEE regulator / lipid binding | ||||||
Function / homology | T3SS negative regulator GrlR / T3SS negative regulator GrlR domain superfamily / Lipocalin / Beta Barrel / Mainly Beta / (2R)-2-HYDROXY-3-(PHOSPHONOOXY)PROPYL HEXANOATE / L0044 / GrlR Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Jobichen, C. / Sivaraman, J. | ||||||
Citation | Journal: Biochem.J. / Year: 2009 Title: Identification and characterization of the lipid binding property of GrlR, a locus of enterocyte effacement regulator. Authors: Jobichen, C. / Fernandis, A.Z. / Velazquez-Campoy, A. / Leung, K.Y. / Mok, Y.K. / Wenk, M.R. / Sivaraman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e3c.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e3c.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 3e3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e3c_validation.pdf.gz | 781.1 KB | Display | wwPDB validaton report |
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Full document | 3e3c_full_validation.pdf.gz | 794.6 KB | Display | |
Data in XML | 3e3c_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 3e3c_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/3e3c ftp://data.pdbj.org/pub/pdb/validation_reports/e3/3e3c | HTTPS FTP |
-Related structure data
Related structure data | 2ovsS 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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-Components
#1: Protein | Mass: 13235.131 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECs4578 / Plasmid: pETM32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O85638, UniProt: Q7DB61*PLUS #2: Chemical | #3: 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: 2.28 Å3/Da / Density % sol: 45.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% ethylene Glycol, 4% Tertiary Butanol, 4% triflouroethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2007 / Details: Mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. all: 8751 / Num. obs: 8472 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.248 / Num. unique all: 781 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2OVS Resolution: 2.5→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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