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Yorodumi- PDB-5dji: Structure of M. tuberculosis CysQ, a PAP phosphatase with AMP, PO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dji | ||||||
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Title | Structure of M. tuberculosis CysQ, a PAP phosphatase with AMP, PO4, and 2Mg bound | ||||||
Components | 3'-phosphoadenosine 5'-phosphate phosphatase | ||||||
Keywords | HYDROLASE / CysQ / PAP phosphatase / AMP / magnesium | ||||||
Function / homology | Function and homology information 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 | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.659 Å | ||||||
Authors | Fisher, A.J. / Erickson, A.I. | ||||||
Citation | Journal: Biochemistry / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dji.cif.gz | 122.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dji.ent.gz | 91.5 KB | Display | PDB format |
PDBx/mmJSON format | 5dji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dji_validation.pdf.gz | 804.8 KB | Display | wwPDB validaton report |
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Full document | 5dji_full_validation.pdf.gz | 806.1 KB | Display | |
Data in XML | 5dji_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 5dji_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/5dji ftp://data.pdbj.org/pub/pdb/validation_reports/dj/5dji | HTTPS FTP |
-Related structure data
Related structure data | 5djfSC 5djgC 5djhC 5djjC 5djkC S: Starting model for refinement C: citing same article (ref.) |
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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: 30746.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cysQ, MT2189 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) 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: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.99 % |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å |
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: 1.659→38.252 Å / Num. obs: 28723 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 38.81 |
Reflection shell | Resolution: 1.659→1.7 Å / Redundancy: 2.49 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 9.17 / % possible all: 84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5DJF Resolution: 1.659→38.252 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 14.93 / 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: 1.659→38.252 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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