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Yorodumi- PDB-4piw: Crystal structure of sugar aminotransferase WecE from Escherichia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4piw | |||||||||
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Title | Crystal structure of sugar aminotransferase WecE from Escherichia coli K-12 | |||||||||
Components | TDP-4-keto-6-deoxy-D-glucose transaminase family protein | |||||||||
Keywords | TRANSFERASE / sugar aminotransferase / Structural Genomics / PSI-Biology / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro | |||||||||
Function / homology | Function and homology information dTDP-4-amino-4,6-dideoxygalactose transaminase / dTDP-4-amino-4,6-dideoxygalactose transaminase activity / enterobacterial common antigen biosynthetic process / polysaccharide biosynthetic process / pyridoxal phosphate binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Wang, F. / Xu, W. / Helmich, K.E. / Singh, S. / Yennamalli, R.M. / Miller, M.D. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) | |||||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of sugar aminotransferase WecE from Escherichia coli K-12 Authors: Wang, F. / Xu, W. / Helmich, K.E. / Singh, S. / Yennamalli, R.M. / Bingman, C.A. / Miller, M.D. / Thorson, J.S. / Phillips Jr., G.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4piw.cif.gz | 564.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4piw.ent.gz | 468.7 KB | Display | PDB format |
PDBx/mmJSON format | 4piw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/4piw ftp://data.pdbj.org/pub/pdb/validation_reports/pi/4piw | HTTPS FTP |
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-Related structure data
Related structure data | 1mdoS 3dr7S 3frkS 4lc3S 4ocaS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 44955.012 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: wecE / Production host: Escherichia coli (E. coli) / References: UniProt: N2U028, UniProt: P27833*PLUS #2: 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: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein solution (10~25 mg/ml, 25 mM Tris or HEPES pH 7.5, 150 mM NaCl) mixed in a 1:1 ratio with the well solution (0.1 M Sodium Acetate, 0.1 M MES pH6.5, 30% (w/v) PEG 2000 MME), ...Details: Protein solution (10~25 mg/ml, 25 mM Tris or HEPES pH 7.5, 150 mM NaCl) mixed in a 1:1 ratio with the well solution (0.1 M Sodium Acetate, 0.1 M MES pH6.5, 30% (w/v) PEG 2000 MME), cryoprotected with 27% PEG 2000 MME and 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2004 |
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.15 |
Reflection | Resolution: 2.7→48.8 Å / Num. all: 275071 / Num. obs: 90907 / % possible obs: 84.23 % / Redundancy: 3 % / Rmerge(I) obs: 0.1109 / Net I/σ(I): 10.31 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ensemble model of 1MDO, 3DR7, 3FRK, 4LC3 and 4OCA Resolution: 2.7→48.801 Å / Cross valid method: FREE R-VALUE / σ(F): 0.25 / Phase error: 34.67 / Stereochemistry target values: TWIN_LSQ_F Details: THE ACTIVE SITE CONTENTS ARE LIKELY TO BE A MIXTURE OF NON-BOUND PLP, COVALENTLY BOUND LYSINE-PLP AND PMP. ONLY COVALENTLY BOUND LYSINE-PLP (LLP) WAS BUILT IN DUE TO THE DATA RESOLUTION LIMIT.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.93 Å2 / Biso mean: 41.2807 Å2 / Biso min: 5.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→48.801 Å
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Refine LS restraints |
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LS refinement shell |
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