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Yorodumi- PDB-3zoz: The structure of human phosphoglycerate kinase with bound bromide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zoz | ||||||
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Title | The structure of human phosphoglycerate kinase with bound bromide, a stimulating anion. | ||||||
Components | PHOSPHOGLYCERATE KINASE 1 | ||||||
Keywords | TRANSFERASE / PHOSPHORYL TRANSFER / ANION STIMULATION / ALLOSTERIC | ||||||
Function / homology | Function and homology information Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis ...Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis / phosphorylation / gluconeogenesis / glycolytic process / ADP binding / cellular response to hypoxia / membrane raft / extracellular space / extracellular exosome / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Bowler, M.W. | ||||||
Citation | Journal: To be Published Title: Identification of the Activating Anion Binding Site in Human Phosphoglycerate Kinase Authors: Bowler, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zoz.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zoz.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zoz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zoz_validation.pdf.gz | 757.5 KB | Display | wwPDB validaton report |
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Full document | 3zoz_full_validation.pdf.gz | 758.7 KB | Display | |
Data in XML | 3zoz_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 3zoz_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/3zoz ftp://data.pdbj.org/pub/pdb/validation_reports/zo/3zoz | HTTPS FTP |
-Related structure data
Related structure data | 2wzcS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44672.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00558, phosphoglycerate kinase |
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-Non-polymers , 6 types, 436 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-BR / |
#4: Chemical | ChemComp-MGF / |
#5: Chemical | ChemComp-3PG / |
#6: Chemical | ChemComp-ADP / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 35% PEG2000MME, 0.1M BIS-TRIS PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.916 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 24, 2009 / Details: MIRROR |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→54 Å / Num. obs: 29204 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 7 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WZC Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.144 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.148 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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