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Yorodumi- PDB-7cj5: Crystal structure of homo dimeric D-allulose 3-epimerase from Met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cj5 | ||||||
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Title | Crystal structure of homo dimeric D-allulose 3-epimerase from Methylomonas sp. in complex with D-fructose | ||||||
Components | Epimerase | ||||||
Keywords | ISOMERASE / Epimerase / TIM barrel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methylomonas sp. DH-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yoshida, H. / Yoshihara, A. / Kamitori, S. | ||||||
Citation | Journal: Febs Open Bio / Year: 2021 Title: Crystal structure of a novel homodimeric l-ribulose 3-epimerase from Methylomonus sp. Authors: Yoshida, H. / Yoshihara, A. / Kato, S. / Mochizuki, S. / Akimitsu, K. / Izumori, K. / Kamitori, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cj5.cif.gz | 245.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cj5.ent.gz | 195.1 KB | Display | PDB format |
PDBx/mmJSON format | 7cj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cj5_validation.pdf.gz | 474.5 KB | Display | wwPDB validaton report |
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Full document | 7cj5_full_validation.pdf.gz | 480.1 KB | Display | |
Data in XML | 7cj5_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 7cj5_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/7cj5 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/7cj5 | HTTPS FTP |
-Related structure data
Related structure data | 7cj4C 7cj6C 7cj7C 7cj8C 7cj9C 5zfsS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 1 / Auth seq-ID: 2 - 286 / Label seq-ID: 2 - 286
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32307.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylomonas sp. DH-1 (bacteria) / Gene: AYM39_05640 / Plasmid: PLASMID / Details (production host): pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: A0A172U6X0 |
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-Sugars , 2 types, 3 molecules
#3: Sugar | #5: Sugar | ChemComp-BDF / | |
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-Non-polymers , 3 types, 259 molecules
#2: Chemical | #4: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 1.74 Å3/Da / Density % sol: 29.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: magnesium chloride, Tris, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.94 Å / Num. obs: 42687 / % possible obs: 99.9 % / Redundancy: 7.167 % / Biso Wilson estimate: 25.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.07 / Χ2: 0.935 / Net I/σ(I): 23.22 / Num. measured all: 305959 / Scaling rejects: 3 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 3.64 / Num. measured obs: 3296 / Num. possible: 582 / Num. unique obs: 530 / CC1/2: 1 / Rrim(I) all: 0.017 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZFS Resolution: 1.8→19.94 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.867 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.81 Å2 / Biso mean: 19.37 Å2 / Biso min: 10.63 Å2
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Refinement step | Cycle: final / Resolution: 1.8→19.94 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 2213 / Type: TIGHT THERMAL / Rms dev position: 5.37 Å / Weight position: 0.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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