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Yorodumi- PDB-7c0z: Crystal structure of a dinucleotide-binding protein (Y246A) of AB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c0z | ||||||
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Title | Crystal structure of a dinucleotide-binding protein (Y246A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form II) | ||||||
Components | Sugar ABC transporter, periplasmic sugar-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / c-di-GMP/AMP / Substrate-binding protein / Thermus thermophilus / tRNA synthesis and/or modification / Venus Fly-trap mechanism / UgpB | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / transmembrane transport / Chem-FGO / Sugar ABC transporter, periplasmic sugar-binding protein Function and homology information | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Kanaujia, S.P. / Chandravanshi, M. / Samanta, R. | ||||||
Funding support | India, 1items
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Citation | Journal: Febs J. / Year: 2021 Title: Structural and thermodynamic insights into the novel dinucleotide-binding protein of ABC transporter unveils its moonlighting function. Authors: Chandravanshi, M. / Samanta, R. / Kanaujia, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c0z.cif.gz | 306 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c0z.ent.gz | 249.7 KB | Display | PDB format |
PDBx/mmJSON format | 7c0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/7c0z ftp://data.pdbj.org/pub/pdb/validation_reports/c0/7c0z | HTTPS FTP |
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-Related structure data
Related structure data | 7c0fSC 7c0kC 7c0lC 7c0oC 7c0rC 7c0sC 7c0tC 7c0uC 7c0vC 7c0wC 7c0xC 7c0yC 7c14C 7c15C 7c16C 7c19C 7c1bC 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:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 1 - 391 / Label seq-ID: 3 - 393
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-Components
#1: Protein | Mass: 44412.691 Da / Num. of mol.: 2 / Mutation: Y246A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0379 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q5SLB4 #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | 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: 2.28 Å3/Da / Density % sol: 46.16 % / Description: Monoclinic |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 6.5 Details: 0.2M ammonium phosphate, 0.1M sodium cacodylate pH 6.5, 30% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 14, 2019 / Details: VariMax HF | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.2→65.74 Å / Num. obs: 39359 / % possible obs: 97.9 % / Redundancy: 4.4 % / CC1/2: 0.978 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.091 / Rrim(I) all: 0.197 / Net I/σ(I): 7.1 / Num. measured all: 172451 / Scaling rejects: 83 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7C0F Resolution: 2.2→65.74 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.873 / SU B: 10.261 / SU ML: 0.134 / SU R Cruickshank DPI: 0.0642 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.047 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE 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 max: 51.64 Å2 / Biso mean: 20.675 Å2 / Biso min: 2.96 Å2
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Refinement step | Cycle: final / Resolution: 2.2→65.74 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 11840 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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