+Open data
-Basic information
Entry | Database: PDB / ID: 8x2s | ||||||
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Title | The Crystal Structure of BPGM from Biortus | ||||||
Components | Bisphosphoglycerate mutase | ||||||
Keywords | ISOMERASE / Hydrolase / Glycolysis | ||||||
Function / homology | Function and homology information carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / neuroinflammatory response / establishment of blood-brain barrier / respiratory gaseous exchange by respiratory system / Glycolysis / defense response to protozoan ...carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / neuroinflammatory response / establishment of blood-brain barrier / respiratory gaseous exchange by respiratory system / Glycolysis / defense response to protozoan / oxygen transport / erythrocyte development / glycolytic process / carbohydrate metabolic process / hydrolase activity / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Li, J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: The Crystal Structure of BPGM from Biortus Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Li, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8x2s.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8x2s.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 8x2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8x2s_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8x2s_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8x2s_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 8x2s_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/8x2s ftp://data.pdbj.org/pub/pdb/validation_reports/x2/8x2s | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 1 - 249 / Label seq-ID: 2 - 250
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 30104.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BPGM / Production host: Escherichia coli (E. coli) / References: UniProt: P07738 #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | 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: 2.42 Å3/Da / Density % sol: 49.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: HM(P07738) 0.1M Hepes-NaOH pH 7.2, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953743 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953743 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→43.37 Å / Num. obs: 44995 / % possible obs: 99.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2 / Num. unique obs: 3090 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.37 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.573 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.147 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.064 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→43.37 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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