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Yorodumi- PDB-6nol: Xanthomonas citri Dephospho-PGM in complex with mannose-1-phosphate -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nol | ||||||
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Title | Xanthomonas citri Dephospho-PGM in complex with mannose-1-phosphate | ||||||
Components | Phosphoglucomutase | ||||||
Keywords | ISOMERASE / phosphoglucomutase | ||||||
Function / homology | Function and homology information intramolecular phosphotransferase activity / carbohydrate metabolic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Xanthomonas axonopodis pv. citri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Stiers, K.M. / Beamer, L.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Struct Dyn. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nol.cif.gz | 197.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nol.ent.gz | 153.9 KB | Display | PDB format |
PDBx/mmJSON format | 6nol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/6nol ftp://data.pdbj.org/pub/pdb/validation_reports/no/6nol | HTTPS FTP |
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-Related structure data
Related structure data | 6nn1C 6nn2C 6nnnC 6nnoC 6nnpC 6nnsC 6nntC 6nnuC 6noqC 6np8C 6npxC 6nqeC 6nqfC 6nqgC 5bmnS 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
#1: Protein | Mass: 51351.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria) Strain: 306 / Gene: xanA, XAC3579 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PGN7 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-PEG / |
#4: Sugar | ChemComp-M1P / |
#5: 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: 2.02 Å3/Da / Density % sol: 38.98 % |
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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: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å |
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: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→46.262 Å / Num. obs: 44430 / % possible obs: 99.9 % / Redundancy: 11.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.358 / Rpim(I) all: 0.103 / Rrim(I) all: 0.373 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 9.1 % / Rmerge(I) obs: 2.696 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2414 / CC1/2: 0.352 / Rpim(I) all: 0.894 / Rrim(I) all: 2.85 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BMN Resolution: 1.73→46.262 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 26.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→46.262 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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