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Yorodumi- PDB-1lda: CRYSTAL STRUCTURE OF THE E. COLI GLYCEROL FACILITATOR (GLPF) WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lda | |||||||||
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Title | CRYSTAL STRUCTURE OF THE E. COLI GLYCEROL FACILITATOR (GLPF) WITHOUT SUBSTRATE GLYCEROL | |||||||||
Components | Glycerol uptake facilitator protein | |||||||||
Keywords | TRANSPORT PROTEIN / GLYCEROL-CONDUCTING MEMBRANE CHANNEL PROTEIN | |||||||||
Function / homology | Function and homology information glycerol channel activity / glycerol transmembrane transporter activity / urea transmembrane transporter activity / glycerol transmembrane transport / cellular response to mercury ion / channel activity / membrane => GO:0016020 / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å | |||||||||
Authors | Nollert, P. / Miercke, L.J.W. / O'Connell, J. / Stroud, R.M. | |||||||||
Citation | Journal: Science / Year: 2002 Title: Control of the selectivity of the aquaporin water channel family by global orientational tuning. Authors: Tajkhorshid, E. / Nollert, P. / Jensen, M.O. / Miercke, L.J. / O'Connell, J. / Stroud, R.M. / Schulten, K. #1: Journal: Science / Year: 2000 Title: Structure of a Glycerol-Conducting Channel and the Basis for Its Selectivity Authors: Fu, D. / Libson, A. / Miercke, L.J. / Weitzman, C. / Nollert, P. / Krucinski, J. / Stroud, R.M. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lda.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lda.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 1lda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lda_validation.pdf.gz | 421.2 KB | Display | wwPDB validaton report |
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Full document | 1lda_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | 1lda_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1lda_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/1lda ftp://data.pdbj.org/pub/pdb/validation_reports/ld/1lda | HTTPS FTP |
-Related structure data
Related structure data | 1ldfC 1ldiC 1fx8S C: citing same article (ref.) 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is generated by the crystallographic four-fold axis: X,Y,Z; -X+1, -Y+1,Z; -Y+1, X, Z; Y, -X+1, Z |
-Components
#1: Protein | Mass: 29799.842 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P11244, UniProt: P0AER0*PLUS | ||
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#2: Sugar | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.63 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: GLPF AT 15-20 MG/ML, 28% (W/V) PEG 2000, 100 MM BICINE pH 9.5, 15 % (V/V) GLYCEROL, 35 MM, N-OCTYL-BETA-D-GLUCOSIDE, MGCL2, 5 MM DTT, pH 9.50, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.9 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Oct 7, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 8698 / Num. obs: 8698 / % possible obs: 78.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.918 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.9 |
Reflection shell | Highest resolution: 2.8 Å / Rmerge(I) obs: 0.296 / % possible all: 72.41 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. measured all: 51474 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS Rmerge(I) obs: 0.296 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1FX8 Resolution: 2.8→30 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Rfactor obs: 0.208 / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.208 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |