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Yorodumi- PDB-5t41: Crystal structure of Mycobacterium avium SerB2 mutant S275A/R279A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t41 | ||||||
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Title | Crystal structure of Mycobacterium avium SerB2 mutant S275A/R279A at pH 6.6 with ethylene glycol bound at ACT- I domain | ||||||
Components | Phosphoserine phosphatase | ||||||
Keywords | HYDROLASE / HAD family / phosphoserine phosphatase | ||||||
Function / homology | Function and homology information phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium avium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.149 Å | ||||||
Authors | Shree, S. / Dubey, S. / Ramachandran, R. | ||||||
Funding support | India, 1items
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Citation | Journal: To be published Title: Crystal Structure of Mycobacterium avium SerB2 (MAV_3907) at pH 6.6 Authors: Shree, S. / Ramachandran, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t41.cif.gz | 158.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t41.ent.gz | 125.1 KB | Display | PDB format |
PDBx/mmJSON format | 5t41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t41_validation.pdf.gz | 439.1 KB | Display | wwPDB validaton report |
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Full document | 5t41_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 5t41_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 5t41_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/5t41 ftp://data.pdbj.org/pub/pdb/validation_reports/t4/5t41 | HTTPS FTP |
-Related structure data
Related structure data | 5is2C 5jjbC 3p96S 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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Unit cell |
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-Components
#1: Protein | Mass: 41685.703 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 5-400 / Mutation: G31R, S275A, R279A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium avium (strain 104) (bacteria) Strain: 104 / Gene: serB, MAV_3907 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QJI1, phosphoserine phosphatase |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.48 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 24% PEG 8000, 0.2M Magnesium acetate tetrahydrate, 0.1M HEPES pH 6.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→41.999 Å / Num. obs: 15906 / % possible obs: 95.8 % / Redundancy: 3 % / Net I/σ(I): 6.01 |
Reflection shell | Resolution: 3.15→3.26 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P96 Resolution: 3.149→41.999 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.29 / Stereochemistry target values: ML
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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: 89.83 Å2 / Biso mean: 62.5055 Å2 / Biso min: 27.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.149→41.999 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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