[English] 日本語
Yorodumi- PDB-4v1h: Crystal structure of a mycobacterial ATP synthase rotor ring in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v1h | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a mycobacterial ATP synthase rotor ring in complex with Iodo-Bedaquiline | ||||||
Components | F0F1 ATP SYNTHASE SUBUNIT C | ||||||
Keywords | HYDROLASE / F1FO-ATP SYNTHASE ROTOR / MEMBRANE PROTEIN STRUCTURE | ||||||
Function / homology | F1F0 ATP synthase subunit C / F1FO ATP Synthase / Up-down Bundle / Mainly Alpha / IODO-BEDAQUILINE / : Function and homology information | ||||||
Biological species | MYCOBACTERIUM PHLEI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Preiss, L. / Yildiz, O. / Meier, T. | ||||||
Citation | Journal: To be Published Title: Structure of the Mycobacterial ATP Synthase Fo Rotor Ring in Complex with Iodo-Bedaquiline Authors: Preiss, L. / Langer, J.D. / Yildiz, O. / Koul, A. / Meier, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4v1h.cif.gz | 105 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4v1h.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 4v1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v1h_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4v1h_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4v1h_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 4v1h_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/4v1h ftp://data.pdbj.org/pub/pdb/validation_reports/v1/4v1h | HTTPS FTP |
-Related structure data
Related structure data | 4v1fS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8612.009 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) MYCOBACTERIUM PHLEI (bacteria) References: UniProt: I0RTF3, H+-transporting two-sector ATPase #2: Chemical | #3: Chemical | ChemComp-TAM / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.41 % / Description: NONE |
---|---|
Crystal grow | pH: 8 / Details: pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→37 Å / Num. obs: 31081 / % possible obs: 96.9 % / Observed criterion σ(I): 1.97 / Redundancy: 3.38 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.25 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.37 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.97 / % possible all: 98 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4V1F Resolution: 1.8→37.345 Å / SU ML: 0.32 / σ(F): 1.93 / Phase error: 26.33 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→37.345 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 49.31 Å / Origin y: 71.128 Å / Origin z: 33.1493 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: ALL |