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Yorodumi- PDB-7c0f: Crystal structure of a dinucleotide-binding protein of ABC transp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c0f | ||||||
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Title | Crystal structure of a dinucleotide-binding protein of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form I) | ||||||
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 | Function and homology information maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / transmembrane transport Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å | ||||||
Authors | Kanaujia, S.P. / Chandravanshi, M. | ||||||
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 | 7c0f.cif.gz | 328.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c0f.ent.gz | 264.1 KB | Display | PDB format |
PDBx/mmJSON format | 7c0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c0f_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7c0f_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7c0f_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 7c0f_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/7c0f ftp://data.pdbj.org/pub/pdb/validation_reports/c0/7c0f | HTTPS FTP |
-Related structure data
Related structure data | 7c0kC 7c0lC 7c0oC 7c0rC 7c0sC 7c0tC 7c0uC 7c0vC 7c0wC 7c0xC 7c0yC 7c0zC 7c14C 7c15C 7c16C 7c19C 7c1bC 4mfiS 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: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 395 / Label seq-ID: 3 - 397
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44504.785 Da / Num. of mol.: 2 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 |
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-Non-polymers , 13 types, 450 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-CO2 / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-PEG / #8: Chemical | ChemComp-PDO / | #9: Chemical | #10: Chemical | ChemComp-1PE / | #11: Chemical | #12: Chemical | ChemComp-PGO / | #13: Chemical | ChemComp-PGR / | #14: Water | ChemComp-HOH / | |
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-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: 2.63 Å3/Da / Density % sol: 53.22 % / Description: Monoclinic |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / 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: Mar 23, 2017 / 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: 2.15→66.06 Å / Num. obs: 48571 / % possible obs: 98.2 % / Redundancy: 2.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.104 / Rrim(I) all: 0.148 / Net I/σ(I): 6.9 | |||||||||||||||
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3803 / CC1/2: 0.697 / Rpim(I) all: 0.41 / Rrim(I) all: 0.594 / % possible all: 95.1 |
-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: 4MFI Resolution: 2.15→66.06 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.219 / SU ML: 0.088 / SU R Cruickshank DPI: 0.0441 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.037 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: 90.29 Å2 / Biso mean: 23.322 Å2 / Biso min: 8.62 Å2
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Refinement step | Cycle: final / Resolution: 2.15→66.06 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 12459 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.15→2.206 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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