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Yorodumi- PDB-6ydm: beta-phosphoglucomutase from Lactococcus lactis with citrate, tri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ydm | |||||||||||||||||||||
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Title | beta-phosphoglucomutase from Lactococcus lactis with citrate, tris and acetate bound | |||||||||||||||||||||
Components | Beta-phosphoglucomutase | |||||||||||||||||||||
Keywords | ISOMERASE / cis-trans proline isomerization / allomorphy / phosphoryl transfer / citrate | |||||||||||||||||||||
Function / homology | Function and homology information beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Lactococcus lactis subsp. lactis (lactic acid bacteria) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | |||||||||||||||||||||
Authors | Wood, H.P. / Cruz-Navarrete, F.A. / Baxter, N.J. / Trevitt, C.R. / Robertson, A.J. / Dix, S.R. / Hounslow, A.M. / Cliff, M.J. / Waltho, J.P. | |||||||||||||||||||||
Funding support | United Kingdom, Mexico, 6items
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Citation | Journal: Nat Commun / Year: 2020 Title: Allomorphy as a mechanism of post-translational control of enzyme activity. Authors: Wood, H.P. / Cruz-Navarrete, F.A. / Baxter, N.J. / Trevitt, C.R. / Robertson, A.J. / Dix, S.R. / Hounslow, A.M. / Cliff, M.J. / Waltho, J.P. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ydm.cif.gz | 316.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ydm.ent.gz | 253.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ydm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ydm_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6ydm_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6ydm_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 6ydm_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/6ydm ftp://data.pdbj.org/pub/pdb/validation_reports/yd/6ydm | HTTPS FTP |
-Related structure data
Related structure data | 6ydjC 6ydkC 6ydlC 2wheS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains A B) |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 24239.594 Da / Num. of mol.: 2 / Mutation: K125R, Y206H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (strain IL1403) (lactic acid bacteria) Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase |
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-Non-polymers , 7 types, 194 molecules
#2: Chemical | ChemComp-CIT / | ||||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PDO / | #6: Chemical | ChemComp-TRS / | #7: Chemical | ChemComp-EDO / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 9.86 Å3/Da / Density % sol: 87.52 % / Description: Rod shaped. |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, sodium acetate (200 mM), TRIS (100 mM), HEPES (50 mM), magnesium chloride (5 mM), EDTA (1 mM), sodium azide (2 mM), trisodium citrate (50 mM), beta-phosphoglucomutase (0.6 mM) PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97179 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97179 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.1→117.3 Å / Num. obs: 27995 / % possible obs: 97.5 % / Redundancy: 8.6 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.033 / Rrim(I) all: 0.098 / Net I/σ(I): 13.7 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WHE Resolution: 2.1→46.61 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 11.717 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.23 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.766 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→46.61 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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