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Open data
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Basic information
Entry | Database: PDB / ID: 5jjb | ||||||
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Title | Crystal structure of Mycobacterium avium SerB2 mutant D343G | ||||||
![]() | Phosphoserine phosphatase | ||||||
![]() | HYDROLASE / HAD family / phosphoserine phosphatase | ||||||
Function / homology | ![]() phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shree, S. / Dubey, S. / Ramachandran, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Mycobacterium avium SerB2 (MAV_3907) at pH 6.6 Authors: Shree, S. / Ramachandran, R. #1: ![]() Title: SAD phasing using iodide ions in a high-throughput structural genomics environment. Authors: Abendroth, J. / Gardberg, A.S. / Robinson, J.I. / Christensen, J.S. / Staker, B.L. / Myler, P.J. / Stewart, L.J. / Edwards, T.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165 KB | Display | ![]() |
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PDB format | ![]() | 129.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5is2C ![]() 5t41C ![]() 3p96S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41729.785 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 5-400 / Mutation: D343G,G31R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 104 / Gene: serB, MAV_3907 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 22-23% PEG 8000, 0.1M Magnesium acetate tetrahydrate, 0.1M HEPES pH 6.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→36.88 Å / Num. obs: 20917 / % possible obs: 96.2 % / Redundancy: 7.7 % / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.31→2.35 Å |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3P96 Resolution: 2.305→36.88 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 28.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.88 Å2 / Biso mean: 48.7134 Å2 / Biso min: 26.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.305→36.88 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: 14
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Refinement TLS params. | Method: refined / Origin x: -5.1826 Å / Origin y: -11.0475 Å / Origin z: -38.7653 Å
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Refinement TLS group | Selection details: all |