[English] 日本語
Yorodumi- PDB-7tce: Crystal structure of delta sub IV Rhodobacter Sphaeroides bc1 wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tce | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of delta sub IV Rhodobacter Sphaeroides bc1 with the antimalarial drug atovaquone. | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE / Respiratory Chain Complex III / Anti-malarial Atovaquone / Rhodobacter Spaheroides bc1 / Inhibition / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Cereibacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.85 Å | ||||||
Authors | Esser, L. / Xia, D. / Zhou, F. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of delta sub IV Rhodobacter Sphaeroides bc1 with the antimalarial drug atovaquone. Authors: Esser, L. / Xia, D. / Zhou, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7tce.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7tce.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7tce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tce_validation.pdf.gz | 5.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7tce_full_validation.pdf.gz | 5.9 MB | Display | |
Data in XML | 7tce_validation.xml.gz | 120 KB | Display | |
Data in CIF | 7tce_validation.cif.gz | 157.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/7tce ftp://data.pdbj.org/pub/pdb/validation_reports/tc/7tce | HTTPS FTP |
-Related structure data
Related structure data | 5kkzS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-Components
-Protein , 3 types, 12 molecules AEKOBFLPCGMQ
#1: Protein | Mass: 50087.422 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: petB, fbcB / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: Q02761 #2: Protein | Mass: 29373.953 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: A3PFR5 #3: Protein | Mass: 19928.375 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: petA, fbcF / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: Q02762, quinol-cytochrome-c reductase |
---|
-Sugars , 1 types, 4 molecules
#8: Sugar | ChemComp-BOG / |
---|
-Non-polymers , 6 types, 30 molecules
#4: Chemical | ChemComp-HEM / #5: Chemical | ChemComp-AOQ / #6: Chemical | ChemComp-6PE / #7: Chemical | ChemComp-SR / #9: Chemical | ChemComp-HEC / #10: Chemical | ChemComp-FES / |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.02 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 7% PEG400, 200 MM HISTIDINE, 150 MM NACL, 10 MM SODIUM ASCORBATE, Atovaquone 5 fold molar excess, B-OG, SUCROSE MONO CAPARATE, TRIS PH 8.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 29, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.85→50 Å / Num. obs: 50477 / % possible obs: 94.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 152.55 Å2 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.096 / Rrim(I) all: 0.223 / Χ2: 1.007 / Net I/σ(I): 3.9 / Num. measured all: 242827 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5kkz Resolution: 3.85→39.43 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 0.37 / Phase error: 34.15 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 475.04 Å2 / Biso mean: 192.085 Å2 / Biso min: 108.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.85→39.43 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
|