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Yorodumi- PDB-2h4z: Human bisphosphoglycerate mutase complexed with 2,3-bisphosphogly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h4z | ||||||
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Title | Human bisphosphoglycerate mutase complexed with 2,3-bisphosphoglycerate | ||||||
Components | Bisphosphoglycerate mutase | ||||||
Keywords | ISOMERASE / BISPHOSPHOGLYCERATE MUTASE / 2 / 3-BISPHOSPHOGLYCERATE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wang, Y. / Gong, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Seeing the process of histidine phosphorylation in human bisphosphoglycerate mutase. Authors: Wang, Y. / Liu, L. / Wei, Z. / Cheng, Z. / Lin, Y. / Gong, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h4z.cif.gz | 126.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h4z.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 2h4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h4z_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2h4z_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2h4z_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 2h4z_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/2h4z ftp://data.pdbj.org/pub/pdb/validation_reports/h4/2h4z | HTTPS FTP |
-Related structure data
Related structure data | 2a9jC 2f90C 2h4xC 2hhjC 1t8pS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31118.375 Da / Num. of mol.: 2 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: P07738, bisphosphoglycerate mutase, EC: 5.4.2.1, EC: 3.1.3.13 #2: Chemical | #3: 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: 2.12 Å3/Da / Density % sol: 41.56 % |
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Crystal grow | Temperature: 277 K / pH: 7 Details: PEG6000, HEPES , VAPOR DIFFUSION, HANGING DROP, pH 7.00, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 13, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 37662 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.6 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1T8P Resolution: 2→28.37 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 255021.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.81 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→28.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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