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Yorodumi- PDB-8a1z: Crystal structure of Phosphoserine phosphatase SerB from Mycobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a1z | ||||||
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Title | Crystal structure of Phosphoserine phosphatase SerB from Mycobacterium avium in complex with 1-(2,4-dichlorophenyl)-3-hydroxyurea | ||||||
Components | Phosphoserine phosphatase | ||||||
Keywords | HYDROLASE / phosphoserine phosphatase / fragment / avium | ||||||
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 / Resolution: 2.28 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 | 8a1z.cif.gz | 197.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a1z.ent.gz | 132.6 KB | Display | PDB format |
PDBx/mmJSON format | 8a1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a1z_validation.pdf.gz | 719.2 KB | Display | wwPDB validaton report |
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Full document | 8a1z_full_validation.pdf.gz | 726.4 KB | Display | |
Data in XML | 8a1z_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 8a1z_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/8a1z ftp://data.pdbj.org/pub/pdb/validation_reports/a1/8a1z | HTTPS FTP |
-Related structure data
Related structure data | 8a21C 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 on special symmetry positions |
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-Components
#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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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-KVU / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 0.1 M MES monohydrate pH 6.1, 16% PEG 6000, 0.2 M magnesium chloride hexahydrate |
-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: Jul 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→43.59 Å / Num. obs: 22525 / % possible obs: 98.82 % / Redundancy: 13.1 % / Biso Wilson estimate: 48.04 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1156 / Rpim(I) all: 0.0332 / Rrim(I) all: 0.1203 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.718 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 1985 / CC1/2: 0.656 / CC star: 0.89 / Rpim(I) all: 0.5093 / % possible all: 88.62 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3p96 Resolution: 2.28→43.59 Å / SU ML: 0.3588 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.6763 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 61.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→43.59 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 28.7103375344 Å / Origin y: 43.1773359021 Å / Origin z: 27.6445515325 Å
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Refinement TLS group | Selection details: all |