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Yorodumi- PDB-1t3d: Crystal structure of Serine Acetyltransferase from E.coli at 2.2A -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t3d | ||||||
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Title | Crystal structure of Serine Acetyltransferase from E.coli at 2.2A | ||||||
Components | Serine acetyltransferase | ||||||
Keywords | TRANSFERASE / left-handed-beta-helix / dimer of trimers | ||||||
Function / homology | Function and homology information cysteine synthase complex / serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine biosynthetic process from serine / response to X-ray / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Pye, V.E. / Tingey, A.P. / Robson, R.L. / Moody, P.C.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The Structure and Mechanism of Serine Acetyltransferase from Escherichia coli Authors: Pye, V.E. / Tingey, A.P. / Robson, R.L. / Moody, P.C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t3d.cif.gz | 162.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t3d.ent.gz | 136.6 KB | Display | PDB format |
PDBx/mmJSON format | 1t3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t3d_validation.pdf.gz | 405.2 KB | Display | wwPDB validaton report |
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Full document | 1t3d_full_validation.pdf.gz | 416.4 KB | Display | |
Data in XML | 1t3d_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 1t3d_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/1t3d ftp://data.pdbj.org/pub/pdb/validation_reports/t3/1t3d | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31581.611 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CYSE, B3607, C4429, Z5034, ECS4485, SF3646, S4122 / Plasmid: pCOCE3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P0A9D4, serine O-acetyltransferase #2: Chemical | #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: 3 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: MES, MPD, sodium thiocyanate, cysteine, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9787 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 51271 / Num. obs: 51271 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5 / Num. unique all: 6351 / % possible all: 77 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→19.96 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.855 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Refinement was carried out in CNS prior to REFMAC with a randomly selected cross validation set of 10.1%, 5175 reflections, of data. A set of 10.2%, 712 reflections, was used from the ...Details: Refinement was carried out in CNS prior to REFMAC with a randomly selected cross validation set of 10.1%, 5175 reflections, of data. A set of 10.2%, 712 reflections, was used from the highest shell. R-work=17.5 (18.4 in the highest shell). Free-R=17.7 (19.4 in the highest shell). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 28.188 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å / Luzzati sigma a obs: 0.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.35 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 20
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