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- PDB-1vli: Crystal structure of Spore coat polysaccharide biosynthesis prote... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1vli | ||||||
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Title | Crystal structure of Spore coat polysaccharide biosynthesis protein spsE (BSU37870) from Bacillus subtilis at 2.38 A resolution | ||||||
![]() | Spore coat polysaccharide biosynthesis protein spsE | ||||||
![]() | BIOSYNTHETIC PROTEIN / 2636322 / SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / BSU37870 / SPSE / PSI / Joint Center for Structural Genomics | ||||||
Function / homology | ![]() N-acylneuraminate-9-phosphate synthase activity / glycosylation / carbohydrate biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of Spore coat polysaccharide biosynthesis protein spsE (BSU37870) from Bacillus subtilis at 2.38 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.9 KB | Display | ![]() |
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PDB format | ![]() | 64.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 42867.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 66.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop Details: 18% PEG MME 2000, 0.04M Tris_base, 0.06M Tris Cl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2004 / Details: ADSC Flat mirror | ||||||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.38→29.29 Å / Num. obs: 24673 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 61.62 Å2 / Rsym value: 0.076 / Net I/σ(I): 13.5 | ||||||||||||||||||
Reflection shell | Resolution: 2.38→2.51 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3515 / Rsym value: 0.7 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. A LOW OCCUPIED ZINC WAS TENATIVELY MODELLED TO COORDINATE HIS214 and HIS236 2. THE DENSITY BETWEEN 64-74 APPEARS TO BE CONTINUOUS, HOWEVER, IT IS IMPOSSIBLE TO BUILD ALL THE MISSING ...Details: 1. A LOW OCCUPIED ZINC WAS TENATIVELY MODELLED TO COORDINATE HIS214 and HIS236 2. THE DENSITY BETWEEN 64-74 APPEARS TO BE CONTINUOUS, HOWEVER, IT IS IMPOSSIBLE TO BUILD ALL THE MISSING RESIDUES INTO IT. AS A RESULT, ATOMIC COORDINATES WERE NOT MODELED INTO THIS DENSITY. 3. DIFFICULT TO BUILD LOOPS: 216-220, 244-248. 4. LOOP WITH POOR DENSITY: 293-297. 5. OLIGOMERIC STATE WAS TENATIVELY ASSIGNED AS MONOMER.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.978 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→29.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.442 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -0.3153 Å / Origin y: 27.0739 Å / Origin z: 82.8304 Å
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Refinement TLS group | Selection: ALL |