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- PDB-6npx: Xanthomonas citri Dephospho-PGM in complex with mannose-6-phosphate -
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Open data
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Basic information
Entry | Database: PDB / ID: 6npx | ||||||
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Title | Xanthomonas citri Dephospho-PGM in complex with mannose-6-phosphate | ||||||
![]() | Phosphoglucomutase | ||||||
![]() | ISOMERASE / phosphoglucomutase | ||||||
Function / homology | ![]() intramolecular phosphotransferase activity / carbohydrate metabolic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stiers, K.M. / Beamer, L.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and dynamical description of the enzymatic reaction of a phosphohexomutase. Authors: Stiers, K.M. / Graham, A.C. / Zhu, J.S. / Jakeman, D.L. / Nix, J.C. / Beamer, L.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 | ![]() | 208.2 KB | Display | ![]() |
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PDB format | ![]() | 163.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 787.6 KB | Display | ![]() |
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Full document | ![]() | 789.1 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nn1C ![]() 6nn2C ![]() 6nnnC ![]() 6nnoC ![]() 6nnpC ![]() 6nnsC ![]() 6nntC ![]() 6nnuC ![]() 6nolC ![]() 6noqC ![]() 6np8C ![]() 6nqeC ![]() 6nqfC ![]() 6nqgC ![]() 5bmnS C: citing same article ( S: Starting model for refinement |
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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: 51351.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 306 / Gene: xanA, XAC3579 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-PEG / |
#4: Sugar | ChemComp-M6P / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.63 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 22% PEG 8000, 0.2M MgCl, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jan 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→45.83 Å / Num. obs: 60987 / % possible obs: 78.3 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.045 / Rrim(I) all: 0.115 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.42→1.45 Å / Redundancy: 4.9 % / Rmerge(I) obs: 2.034 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3892 / CC1/2: 0.488 / Rpim(I) all: 1.005 / Rrim(I) all: 2.281 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BMN Resolution: 1.42→39.288 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→39.288 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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