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Yorodumi- PDB-4ew7: The crystal structure of conjugative transfer PAS_like domain fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ew7 | |||||||||
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Title | The crystal structure of conjugative transfer PAS_like domain from Salmonella enterica subsp. enterica serovar Typhimurium | |||||||||
Components | Conjugative transfer: regulation | |||||||||
Keywords | TRANSCRIPTION / alpha-beta-alpha structure / Structural Genomics / Midwest Center for Structural Genomics (MCSG) / PSI-Biology / PAS-like fold / cytoplasmic / Program for the Characterization of Secreted Effector Proteins / PCSEP | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 Å | |||||||||
Authors | Wu, R. / Jedrzejczak, R.P. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Adkins, J.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP) | |||||||||
Citation | Journal: To be Published Title: The crystal structure of conjugative transfer PAS_like domain from Salmonella enterica subsp. enterica serovar Typhimurium Authors: Wu, R. / Jedrzejczak, R.P. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Adkins, J.N. / Joachimiak, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ew7.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ew7.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 4ew7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ew7_validation.pdf.gz | 463.6 KB | Display | wwPDB validaton report |
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Full document | 4ew7_full_validation.pdf.gz | 463.9 KB | Display | |
Data in XML | 4ew7_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 4ew7_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/4ew7 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/4ew7 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14772.407 Da / Num. of mol.: 1 Fragment: conjugative transfer PAS_like domain residues 5-128 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria) Strain: 588858 / Gene: STM14_5595, traJ / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 MAGIC / References: UniProt: D0ZHW1, UniProt: A0A0F6AW83*PLUS |
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-Non-polymers , 7 types, 48 molecules
#2: Chemical | ChemComp-SIN / |
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#3: Chemical | ChemComp-ACY / |
#4: Chemical | ChemComp-PYR / |
#5: Chemical | ChemComp-NA / |
#6: Chemical | ChemComp-CL / |
#7: Chemical | ChemComp-GOL / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M DL, malic acid, pH 7.0, 20% PEG 3500, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→50 Å / Num. all: 15181 / Num. obs: 15181 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 26.97 Å2 / Rsym value: 0.049 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.67→1.7 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 659 / Rsym value: 0.452 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.67→27.912 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 17.68 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.573 Å2 / ksol: 0.408 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.67→27.912 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Origin x: -5.8135 Å / Origin y: 40.0919 Å / Origin z: 16.4219 Å
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Refinement TLS group | Selection details: chain A |