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- PDB-1rf5: Structural Studies of Streptococcus pneumoniae EPSP Synthase in U... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rf5 | ||||||
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Title | Structural Studies of Streptococcus pneumoniae EPSP Synthase in Unliganded State | ||||||
![]() | 5-enolpyruvylshikimate-3-phosphate synthase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, H. / Hilsenbeck, J.L. / Kim, H.J. / Shuttleworth, W.A. / Park, Y.H. / Evans, J.N. / Kang, C. | ||||||
![]() | ![]() Title: Structural studies of Streptococcus pneumoniae EPSP synthase in unliganded state, tetrahedral intermediate-bound state and S3P-GLP-bound state. Authors: Park, H. / Hilsenbeck, J.L. / Kim, H.J. / Shuttleworth, W.A. / Park, Y.H. / Evans, J.N. / Kang, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 334.9 KB | Display | ![]() |
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PDB format | ![]() | 274.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | The biological assembly is a monomer |
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Components
#1: Protein | Mass: 45878.820 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9S400, ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.95 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, NaCl, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2001 | ||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→30 Å / Num. all: 102641 / Num. obs: 102641 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 | ||||||||||||
Reflection shell | Resolution: 2.2→2.3 Å / % possible all: 96.5 | ||||||||||||
Reflection | *PLUS Num. measured all: 982621 / Rmerge(I) obs: 0.036 | ||||||||||||
Reflection shell | *PLUS % possible obs: 96.5 % / Rmerge(I) obs: 0.128 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Details: The peptide bond distance between GLU 340 and THR 341 of chains A and C, and between GLU 334 and GLU 335 of chain C, are slightly longer than typical peptide bond distance. Residues 335-340 ...Details: The peptide bond distance between GLU 340 and THR 341 of chains A and C, and between GLU 334 and GLU 335 of chain C, are slightly longer than typical peptide bond distance. Residues 335-340 were set to 0 occupancy and was not included in refinement.
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection all: 95252 / % reflection Rfree: 5 % / Rfactor Rfree![]() | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 2.49 | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.272 / Rfactor Rwork: 0.219 |