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- PDB-5djh: Structure of M. tuberculosis CysQ, a PAP phosphatase with AMP, PO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5djh | ||||||
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Title | Structure of M. tuberculosis CysQ, a PAP phosphatase with AMP, PO4, and 3Mg bound | ||||||
![]() | 3'-phosphoadenosine 5'-phosphate phosphatase | ||||||
![]() | HYDROLASE / CysQ / PAP phosphatase / AMP / magnesium | ||||||
Function / homology | ![]() Sulfate assimilation / 3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / inositol monophosphate 1-phosphatase activity / sulfate assimilation / fructose-bisphosphatase ...Sulfate assimilation / 3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / inositol monophosphate 1-phosphatase activity / sulfate assimilation / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cobalt ion binding / manganese ion binding / magnesium ion binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fisher, A.J. / Erickson, A.I. | ||||||
![]() | ![]() Title: Crystal Structures of Mycobacterium tuberculosis CysQ, with Substrate and Products Bound. Authors: Erickson, A.I. / Sarsam, R.D. / Fisher, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.6 KB | Display | ![]() |
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PDB format | ![]() | 91.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5djfSC ![]() 5djgC ![]() 5djiC ![]() 5djjC ![]() 5djkC 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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Unit cell |
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Components
#1: Protein | Mass: 30746.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P9WKJ0, UniProt: P9WKJ1*PLUS, 3'(2'),5'-bisphosphate nucleotidase, fructose-bisphosphatase, inositol-phosphate phosphatase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-AMP / | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.73 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M magnesium acetate, 0.1 M Bis-Tris-HCl, 35% PEG550 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2014 |
Radiation | Monochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12709 Å / Relative weight: 1 |
Reflection | Resolution: 1.451→38.168 Å / Num. all: 42861 / Num. obs: 42861 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.53 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 23.87 |
Reflection shell | Resolution: 1.451→1.49 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.47 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5DJF Resolution: 1.451→38.168 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 15.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.451→38.168 Å
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Refine LS restraints |
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LS refinement shell |
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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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