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- PDB-3glc: Crystal Structure of E. coli LsrF in complex with Ribose-5-phosphate -
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Open data
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Basic information
Entry | Database: PDB / ID: 3glc | ||||||
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Title | Crystal Structure of E. coli LsrF in complex with Ribose-5-phosphate | ||||||
![]() | Aldolase lsrF | ||||||
![]() | LYASE / TIM barrel / Schiff base | ||||||
Function / homology | ![]() 3-hydroxy-5-phosphooxypentane-2,4-dione thiolase / fructose-bisphosphate aldolase activity / acyltransferase activity, transferring groups other than amino-acyl groups / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Miller, S.T. / Diaz, Z.C. | ||||||
![]() | ![]() Title: The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF. Authors: Diaz, Z. / Xavier, K.B. / Miller, S.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1013.2 KB | Display | ![]() |
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PDB format | ![]() | 850.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 623.1 KB | Display | ![]() |
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Full document | ![]() | 685 KB | Display | |
Data in XML | ![]() | 187.2 KB | Display | |
Data in CIF | ![]() | 244.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gkfSC ![]() 3gndC 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Refine code: 1 / Auth seq-ID: -99999 - 99999 / Label seq-ID: -99999 - 99999
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Details | biological unit is a decamer. There are 2 biological units in the asymmetric unit (Chains ABCDEFGHIJ and chains KLMNOPQRST) |
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Components
#1: Protein | Mass: 32322.145 Da / Num. of mol.: 20 / Fragment: Uncharacterized aldolase LsrF Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P76143, Lyases; Carbon-carbon lyases; Aldehyde-lyases #2: Sugar | ChemComp-R5P / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 4% PEG 400, 100 mM MgCl2, 2.3 M Ammonium Sulfate, pH 7.5, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 18, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→55.73 Å / Num. all: 327170 / Num. obs: 154484 / % possible obs: 81.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 1.8 / Num. unique all: 18764 / % possible all: 67.8 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3GKF Resolution: 2.5→55.73 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.837 / SU B: 10.846 / SU ML: 0.238 / SU Rfree: 0.405 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 108.88 Å2 / Biso mean: 35.975 Å2 / Biso min: 5.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→55.73 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 2127 / Refine-ID: X-RAY DIFFRACTION
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