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Yorodumi- PDB-2wzc: The catalytically active fully closed conformation of human phosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wzc | ||||||
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Title | The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP, 3PG and aluminium tetrafluoride | ||||||
Components | PHOSPHOGLYCERATE KINASE 1 | ||||||
Keywords | TRANSFERASE / HEREDITARY HEMOLYTIC ANEMIA / PHOSPHOPROTEIN / KINASE / GLYCOLYSIS / NUCLEOTIDE-BINDING | ||||||
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 / ADP binding / gluconeogenesis / glycolytic process / cellular response to hypoxia / membrane raft / phosphorylation / extracellular space / extracellular exosome / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Bowler, M.W. / Cliff, M.J. / Marston, J.P.M. / Baxter, N.J. / Hownslow, A.M.H. / Varga, A.V. / Szabo, J. / Vas, M. / Blackburn, G.M. / Waltho, J.P. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Transition State Analogue Structures of Human Phosphoglycerate Kinase Establish the Importance of Charge Balance in Catalysis. Authors: Cliff, M.J. / Bowler, M.W. / Szabo, J. / Marston, J.P.M. / Varga, A.V. / Hownslow, A.M.H. / Baxter, N.J. / Blackburn, G.M. / Vas, M. / Waltho, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wzc.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wzc.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 2wzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/2wzc ftp://data.pdbj.org/pub/pdb/validation_reports/wz/2wzc | HTTPS FTP |
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-Related structure data
Related structure data | 2wzbC 2wzdC 3c39S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44541.426 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-417 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH ADP, 3PG AND ALUMINIUM FLUORIDE / 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, 478 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-ALF / |
#5: Chemical | ChemComp-ADP / |
#6: Chemical | ChemComp-3PG / |
#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: 2.19 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 22% 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: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 22, 2009 / Details: GE211 |
Radiation | Monochromator: C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 61523 / % possible obs: 97.4 % / Observed criterion σ(I): 3 / Redundancy: 2.8 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3C39 Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.444 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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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: 6.404 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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