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Yorodumi- PDB-8a21: Crystal structure of Phosphoserine phosphatase SerB from Mycobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a21 | ||||||
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Title | Crystal structure of Phosphoserine phosphatase SerB from Mycobacterium avium in complex with phenylimidazole | ||||||
Components | Phosphoserine phosphatase | ||||||
Keywords | HYDROLASE / phosphoserine phosphatase / avium / PIM / phenylimidazole | ||||||
Function / homology | Function and homology information phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium avium 104 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.18 Å | ||||||
Authors | Haufroid, M. / Wouters, J. | ||||||
Funding support | 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2022 Title: Targeting the phosphoserine phosphatase MtSerB2 for tuberculosis drug discovery, an hybrid knowledge based /fragment based approach. Authors: Haufroid, M. / Volkov, A.N. / Wouters, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a21.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a21.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 8a21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a21_validation.pdf.gz | 659.7 KB | Display | wwPDB validaton report |
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Full document | 8a21_full_validation.pdf.gz | 670.3 KB | Display | |
Data in XML | 8a21_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 8a21_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/8a21 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/8a21 | HTTPS FTP |
-Related structure data
Related structure data | 8a1zC 3p96S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43852.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium avium 104 (bacteria) / Gene: O972_03940 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V7LE91, phosphoserine phosphatase |
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-Non-polymers , 5 types, 216 molecules
#2: Chemical | ChemComp-MG / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.57 Å3/Da / Density % sol: 52.2 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: MgCl2 0,5M; 20%PEG6000 MES 0.1M pH6.1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→43.09 Å / Num. obs: 25224 / % possible obs: 98.76 % / Redundancy: 13.3 % / Biso Wilson estimate: 35.66 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1115 / Rpim(I) all: 0.0319 / Rrim(I) all: 0.1161 / Net I/σ(I): 16.22 |
Reflection shell | Resolution: 2.18→2.26 Å / Redundancy: 11.6 % / Rmerge(I) obs: 1.531 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 2238 / CC1/2: 0.777 / CC star: 0.935 / Rpim(I) all: 0.4595 / % possible all: 87.94 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3p96 Resolution: 2.18→43.09 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.59 / 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: 69.82 Å2 / Biso mean: 37.0195 Å2 / Biso min: 16.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.18→43.09 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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