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Yorodumi- PDB-6noq: Xanthomonas citri Phospho-PGM in complex with mannose-1-phosphate -
+Open data
-Basic information
Entry | Database: PDB / ID: 6noq | ||||||
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Title | Xanthomonas citri Phospho-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 / Resolution: 1.61 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 | 6noq.cif.gz | 194.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6noq.ent.gz | 155.9 KB | Display | PDB format |
PDBx/mmJSON format | 6noq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/6noq ftp://data.pdbj.org/pub/pdb/validation_reports/no/6noq | HTTPS FTP |
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-Related structure data
Related structure data | 6nn1C 6nn2C 6nnnC 6nnoC 6nnpC 6nnsC 6nntC 6nnuC 6nolC 6np8C 6npxC 6nqeC 6nqfC 6nqgC 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: 51431.621 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: Sugar | ChemComp-M1P / |
#4: 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: 39.01 % |
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Crystal grow | Temperature: 277 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: 1.61→46.253 Å / Num. obs: 55020 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.311 / Rpim(I) all: 0.092 / Rrim(I) all: 0.324 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.61→1.64 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.784 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2656 / CC1/2: 0.348 / Rpim(I) all: 0.652 / Rrim(I) all: 1.904 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Resolution: 1.61→46.253 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 27.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→46.253 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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