+Open data
-Basic information
Entry | Database: PDB / ID: 5it4 | ||||||
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Title | Crystal structure of Mycobacterium avium SerB2 mutant D343N | ||||||
Components | Phosphoserine phosphatase | ||||||
Keywords | HYDROLASE / HAD family / phosphoserine phosphatase / catalytic site mutant | ||||||
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: 2.102 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 mutant D343N (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 | 5it4.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5it4.ent.gz | 130.2 KB | Display | PDB format |
PDBx/mmJSON format | 5it4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5it4_validation.pdf.gz | 424.2 KB | Display | wwPDB validaton report |
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Full document | 5it4_full_validation.pdf.gz | 426 KB | Display | |
Data in XML | 5it4_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 5it4_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/5it4 ftp://data.pdbj.org/pub/pdb/validation_reports/it/5it4 | HTTPS FTP |
-Related structure data
Related structure data | 3p96S S: Starting model for refinement |
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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: 41786.836 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 5-400 / Mutation: G31R, D343N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium avium (strain 104) (bacteria) Strain: 104 / Gene: serB, MAV_3907 / 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: 2.88 Å3/Da / Density % sol: 57.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 22- 23% PEG 8000, 0.1 M Magnesium acetate tetrahydrate, 0.1 M HEPES pH 6.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 28166 / % possible obs: 98.6 % / Redundancy: 7.9 % / Net I/σ(I): 27.625 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P96 Resolution: 2.102→30.626 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 25.61 / 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: 106.82 Å2 / Biso mean: 47.5627 Å2 / Biso min: 27.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.102→30.626 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: -5.095 Å / Origin y: -10.7597 Å / Origin z: -38.967 Å
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Refinement TLS group | Selection details: all |