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Yorodumi- PDB-7qpl: Crystal structure of phosphoserine phosphatase (SerB) from Brucel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qpl | ||||||
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Title | Crystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis in complex with phosphate and magnesium | ||||||
Components | O-phosphoserine phosphohydrolase | ||||||
Keywords | HYDROLASE / HAD phosphatase / ACT-like domain / Rossmanoid fold / L-serine biosynthesis | ||||||
Function / homology | Function and homology information phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Brucella melitensis bv. 1 str. 16M (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Pierson, E. / Wouters, J. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: To Be Published Title: Crystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis in complex with phosphate and magnesium Authors: Pierson, E. / Wouters, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qpl.cif.gz | 154.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qpl.ent.gz | 106.2 KB | Display | PDB format |
PDBx/mmJSON format | 7qpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qpl_validation.pdf.gz | 585.4 KB | Display | wwPDB validaton report |
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Full document | 7qpl_full_validation.pdf.gz | 588.5 KB | Display | |
Data in XML | 7qpl_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 7qpl_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/7qpl ftp://data.pdbj.org/pub/pdb/validation_reports/qp/7qpl | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32549.479 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SerB sequence is preceded by the rest of HRV-3C protease cleavage site (GPGS) at N-term Source: (gene. exp.) Brucella melitensis bv. 1 str. 16M (bacteria) Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEI0615 / Plasmid: AVA0421 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8YI30, phosphoserine phosphatase |
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-Non-polymers , 7 types, 296 molecules
#2: Chemical | ChemComp-PEG / | ||||||||||
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#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-FMT / #5: Chemical | #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-PO4 / | #8: 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: 3.54 Å3/Da / Density % sol: 65.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.2M Sodium Formate, 0.1M Sodium phosphate pH 6.8, 22% w/v BCS PEG smear MMW, 10% v/v glycerol PH range: 6.6-7.0 / Temp details: Room temperature |
-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: 0.978565 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978565 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→38.27 Å / Num. obs: 47522 / % possible obs: 95.42 % / Redundancy: 41.4 % / Biso Wilson estimate: 39.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09586 / Rpim(I) all: 0.01509 / Rrim(I) all: 0.09705 / Net I/σ(I): 22.77 |
Reflection shell | Resolution: 1.77→1.833 Å / Redundancy: 41.3 % / Rmerge(I) obs: 2.942 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 2558 / CC1/2: 0.616 / Rpim(I) all: 0.4624 / Rrim(I) all: 2.978 / % possible all: 54.56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Alphafold model Resolution: 1.77→38.27 Å / SU ML: 0.1984 / Cross valid method: FREE R-VALUE / Phase error: 21.7719 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: 54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→38.27 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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