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Yorodumi- PDB-3gnd: Crystal Structure of E. coli LsrF in complex with Ribulose-5-phosphate -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gnd | ||||||
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Title | Crystal Structure of E. coli LsrF in complex with Ribulose-5-phosphate | ||||||
Components | Aldolase lsrF | ||||||
Keywords | LYASE / TIM barrel / Schiff base | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å | ||||||
Authors | Miller, S.T. / Diaz, Z.C. | ||||||
Citation | Journal: Plos One / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gnd.cif.gz | 1020.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gnd.ent.gz | 853.2 KB | Display | PDB format |
PDBx/mmJSON format | 3gnd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/3gnd ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gnd | HTTPS FTP |
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-Related structure data
Related structure data | 3gkfSC 3glcC S: Starting model for refinement C: citing same article (ref.) |
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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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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) |
-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.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1517, JW1510, lsrF, yneB / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 References: UniProt: P76143, Lyases; Carbon-carbon lyases; Aldehyde-lyases #2: Sugar | ChemComp-5RP / #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: 45.94 % |
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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: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: Oct 18, 2008 / Details: Si(111) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.9→49.03 Å / Num. all: 111445 / Num. obs: 111445 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.09 / Χ2: 1.219 / Net I/σ(I): 8.666 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3GKF Resolution: 2.9→49.03 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 1 / SU B: 38.671 / SU ML: 0.318 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
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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: 99.65 Å2 / Biso mean: 25.53 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→49.03 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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