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Yorodumi- PDB-3lnw: Close correlation of protein thermostability and self-buried area... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lnw | ||||||
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Title | Close correlation of protein thermostability and self-buried area rate revealed by crystal structure of HPr from Thermoanaerobacter tengcongensis MB4 | ||||||
Components | Phosphotransferase system, HPr-related proteinsPEP group translocation | ||||||
Keywords | TRANSFERASE / HPr / thermostability mechanism / self-buried area / hydrophobic effect / Thermoanaerobacter tengcongensis / Kinase / Phosphotransferase system | ||||||
Function / homology | Function and homology information Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Thermoanaerobacter tengcongensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.302 Å | ||||||
Authors | Gao, G.G. / Feng, C. / Gao, F. / Liu, Y. | ||||||
Citation | Journal: To be Published Title: Close correlation of protein thermostability and self-buried area rate revealed by crystal structure of HPr from Thermoanaerobacter tengcongensis MB4 Authors: Gao, G.G. / Feng, C. / Gao, F. / Liu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lnw.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lnw.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lnw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/3lnw ftp://data.pdbj.org/pub/pdb/validation_reports/ln/3lnw | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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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: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 1 - 86 / Label seq-ID: 1 - 86
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-Components
#1: Protein | Mass: 9620.015 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria) Strain: MB4 / Gene: FruB, TTE1820 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8R910 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 24 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.485 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 11556 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 24.271 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 8.404 / Num. unique all: 63655 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.302→38.304 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0.16 / Phase error: 24.46 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.915 Å2 / ksol: 0.366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.8 Å2 / Biso mean: 31.204 Å2 / Biso min: 12.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2.302→38.304 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Origin x: -10.9682 Å / Origin y: -19.0853 Å / Origin z: 10.7994 Å
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Refinement TLS group |
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