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- PDB-4ng4: Structure of phosphoglycerate kinase (CBU_1782) from Coxiella burnetii -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ng4 | ||||||
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Title | Structure of phosphoglycerate kinase (CBU_1782) from Coxiella burnetii | ||||||
![]() | Phosphoglycerate kinase | ||||||
![]() | TRANSFERASE / phosphoglycerate kinase | ||||||
Function / homology | ![]() phosphoglycerate kinase / phosphoglycerate kinase activity / positive regulation of oxidative phosphorylation / gluconeogenesis / glycolytic process / ADP binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Franklin, M.C. / Cheung, J. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J. | ||||||
![]() | ![]() Title: Structural genomics for drug design against the pathogen Coxiella burnetii. Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 446.5 KB | Display | ![]() |
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PDB format | ![]() | 368.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 42 KB | Display | |
Data in CIF | ![]() | 56.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tq8C ![]() 3tq9C ![]() 3tqaC ![]() 3tqbC ![]() 3tqcC ![]() 3tqdC ![]() 3tqeC ![]() 3tqfC ![]() 3tqgC ![]() 3tqhC ![]() 3tqiC ![]() 3tqjC ![]() 3tqlC ![]() 3tqmC ![]() 3tqnC ![]() 3tqoC ![]() 3tqpC ![]() 3tqqC ![]() 3tqrC ![]() 3tqsC ![]() 3tqtC ![]() 3tquC ![]() 3tqwC ![]() 3tqxC ![]() 3tqyC ![]() 3tqzC ![]() 3tr0C ![]() 3tr1C ![]() 3tr2C ![]() 3tr3C ![]() 3tr4C ![]() 3tr5C ![]() 3tr6C ![]() 3tr7C ![]() 3tr8C ![]() 3tr9C ![]() 3trbC ![]() 3trcC ![]() 3trdC ![]() 3treC ![]() 3trfC ![]() 3trgC ![]() 3trhC ![]() 3triC ![]() 3tthC ![]() 3ty2C ![]() 3uwcC ![]() 4f3qC ![]() 4f3rC ![]() 4nbqC ![]() 1zmrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 43776.285 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: This construct's boundaries were selected based on the GenBank gene sequence. However, the N terminus of the GenBank sequence was later discovered to be incorrect; based on homology to other ...Details: This construct's boundaries were selected based on the GenBank gene sequence. However, the N terminus of the GenBank sequence was later discovered to be incorrect; based on homology to other phosphoglycerate kinases, the correct N terminus is five residues later, i.e. MKALP... Residue numbering in this structure reflects the correct N terminus. Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | Sequence details | THIS CONSTRUCT'S BOUNDARIES WERE SELECTED BASED ON THE GENBANK GENE SEQUENCE. HOWEVER, THE N ...THIS CONSTRUCT'S BOUNDARIES | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Sodium chloride, HEPES, PEG 3000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→50 Å / Num. all: 30881 / Num. obs: 30663 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.129 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.78→2.85 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1532 / Rsym value: 0.522 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Homology models of cbu_1782 sequence built on the coordinates of 1ZMR, split into two domains Resolution: 2.78→43.21 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.828 / SU B: 42.915 / SU ML: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.491 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.646 Å2
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Refinement step | Cycle: LAST / Resolution: 2.78→43.21 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.78→2.849 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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