+Open data
-Basic information
Entry | Database: PDB / ID: 1yjx | ||||||
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Title | Crystal structure of human B type phosphoglycerate mutase | ||||||
Components | Phosphoglycerate mutase 1 | ||||||
Keywords | ISOMERASE / HYDROLASE / alpha/beta | ||||||
Function / homology | Function and homology information bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen ...bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen / ficolin-1-rich granule lumen / hydrolase activity / Neutrophil degranulation / protein kinase binding / extracellular exosome / extracellular region / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Wang, Y. / Wei, Z. / Liu, L. / Gong, W. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2005 Title: Crystal structure of human B-type phosphoglycerate mutase bound with citrate. Authors: Wang, Y. / Wei, Z. / Liu, L. / Cheng, Z. / Lin, Y. / Ji, F. / Gong, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yjx.cif.gz | 563.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yjx.ent.gz | 463.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yjx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yjx_validation.pdf.gz | 567.5 KB | Display | wwPDB validaton report |
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Full document | 1yjx_full_validation.pdf.gz | 665.7 KB | Display | |
Data in XML | 1yjx_validation.xml.gz | 117.3 KB | Display | |
Data in CIF | 1yjx_validation.cif.gz | 150.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/1yjx ftp://data.pdbj.org/pub/pdb/validation_reports/yj/1yjx | HTTPS FTP |
-Related structure data
Related structure data | 1yfkC 5pgmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 29917.104 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P18669, EC: 5.4.2.1, bisphosphoglycerate mutase, EC: 3.1.3.13 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-CIT / #4: Water | ChemComp-HOH / | |
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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 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: PEG4000, iso-Propanol, tri-Sodium Citrate dehydrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.978 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 26, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 85016 / Num. obs: 85016 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 60.8 Å2 / Rmerge(I) obs: 0.012 / Net I/σ(I): 8.627 |
Reflection shell | Resolution: 2.8→2.87 Å / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2.22 / Num. unique all: 5585 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5PGM Resolution: 2.8→29.91 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2286036.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 14.9239 Å2 / ksol: 0.301839 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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