+Open data
-Basic information
Entry | Database: PDB / ID: 5is2 | ||||||
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Title | Crystal structure of Mycobacterium avium SerB2 at pH 6.6 | ||||||
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 / dephosphorylation / magnesium ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium avium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.881 Å | ||||||
Authors | Shree, 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. #1: Journal: J. Struct. Funct. Genomics / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5is2.cif.gz | 163.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5is2.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 5is2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5is2_validation.pdf.gz | 424.9 KB | Display | wwPDB validaton report |
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Full document | 5is2_full_validation.pdf.gz | 427.4 KB | Display | |
Data in XML | 5is2_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 5is2_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/5is2 ftp://data.pdbj.org/pub/pdb/validation_reports/is/5is2 | HTTPS FTP |
-Related structure data
Related structure data | 5jjbC 5t41C 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: 41787.820 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 5-400 / Mutation: G31R 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) / Strain (production host): C41(DE3) / References: UniProt: A0QJI1, phosphoserine phosphatase |
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#2: Chemical | ChemComp-MG / |
#3: 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: 2.9 Å3/Da / Density % sol: 57.58 % Description: Mycobacterium avium SerB2 protein was crystallized in presence of its inhibitor rosaniline (a pink color compound) and pink coloured crystals were diffracted, however no density of ...Description: Mycobacterium avium SerB2 protein was crystallized in presence of its inhibitor rosaniline (a pink color compound) and pink coloured crystals were diffracted, however no density of rosaniline was found on solving the crystal data. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 22% 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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 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: 1.88→50 Å / Num. obs: 38932 / % possible obs: 98.4 % / Redundancy: 7.8 % / Net I/σ(I): 29 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P96 Resolution: 1.881→26.139 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 28.81 / 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: 132.75 Å2 / Biso mean: 53.9969 Å2 / Biso min: 28.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.881→26.139 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: -4.9413 Å / Origin y: -10.7168 Å / Origin z: -38.6808 Å
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Refinement TLS group | Selection details: all |