[English] 日本語
![](img/lk-miru.gif)
- PDB-7vf8: Crystal Structure of HasAp with Co-5-octaethyloxaporphyrinium cation -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7vf8 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of HasAp with Co-5-octaethyloxaporphyrinium cation | ||||||||||||||||||||||||
![]() | Heme acquisition protein HasAp | ||||||||||||||||||||||||
![]() | METAL TRANSPORT / Heme acquisition protein | ||||||||||||||||||||||||
Function / homology | Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / metal ion binding / Co-5-octaethyloxaporphyrinium cation / CITRIC ACID / DI(HYDROXYETHYL)ETHER / Heme acquisition protein HasAp![]() | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Takiguchi, A. / Sakakibara, E. / Sugimoto, H. / Shoji, O. / Shinokubo, H. | ||||||||||||||||||||||||
Funding support | ![]()
| ||||||||||||||||||||||||
![]() | ![]() Title: Crystal Structure of HasAp with Co-5-octaethyloxaporphyrinium cation Authors: Takiguchi, A. / Sakakibara, E. / Sugimoto, H. / Shoji, O. / Shinokubo, H. | ||||||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 188.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 151.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5xa4S S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18901.535 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: hasAp, PA3407 / Plasmid: pQE30 / Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 346 molecules ![](data/chem/img/7KI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CIT / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.94 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.0M potassium sodium tartrate, 100mM imidazole/hydrochloric acid (pH 8.0), 200mM sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→44.45 Å / Num. obs: 111120 / % possible obs: 98.5 % / Redundancy: 20.056 % / Biso Wilson estimate: 23.368 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.125 / Χ2: 0.779 / Net I/σ(I): 21.25 / Num. measured all: 2228601 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5XA4 Resolution: 1.35→44.45 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.323 / SU ML: 0.023 / SU R Cruickshank DPI: 0.0396 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 80.63 Å2 / Biso mean: 18.002 Å2 / Biso min: 6.29 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→44.45 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.35→1.384 Å / Rfactor Rfree error: 0
|