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Yorodumi- PDB-7c1b: Crystal structure of a dinucleotide-binding protein (F79A/Y224A/Y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c1b | ||||||
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Title | Crystal structure of a dinucleotide-binding protein (F79A/Y224A/Y246A and deletion of residues 50-75) of ABC transporter (unbound form) | ||||||
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 / DI(HYDROXYETHYL)ETHER / 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: 2.3 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 | 7c1b.cif.gz | 157.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c1b.ent.gz | 121.3 KB | Display | PDB format |
PDBx/mmJSON format | 7c1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/7c1b ftp://data.pdbj.org/pub/pdb/validation_reports/c1/7c1b | HTTPS FTP |
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-Related structure data
Related structure data | 7c0fSC 7c0kC 7c0lC 7c0oC 7c0rC 7c0sC 7c0tC 7c0uC 7c0vC 7c0wC 7c0xC 7c0yC 7c0zC 7c14C 7c15C 7c16C 7c19C 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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Unit cell |
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-Components
#1: Protein | Mass: 41554.344 Da / Num. of mol.: 1 / Mutation: F79A, Y224A, Y246A and deletion of residues 50-75 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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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.17 % / Description: Orthorhombic |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 6.5 Details: 0.2M ammonium sulphate, 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: Dec 8, 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 | Resolution: 2.3→62.2 Å / Num. obs: 16950 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.048 / Rrim(I) all: 0.157 / Net I/σ(I): 11.5 / Num. measured all: 181309 / Scaling rejects: 496 | ||||||||||||||||||||||||||||||
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: 2.3→62.2 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.876 / WRfactor Rfree: 0.2519 / WRfactor Rwork: 0.1827 / FOM work R set: 0.8125 / SU B: 15.515 / SU ML: 0.193 / SU R Cruickshank DPI: 0.3787 / SU Rfree: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.58 Å2 / Biso mean: 30.045 Å2 / Biso min: 10.7 Å2
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Refinement step | Cycle: final / Resolution: 2.3→62.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 26.2028 Å / Origin y: 16.3681 Å / Origin z: 14.2605 Å
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