+
Open data
-
Basic information
Entry | Database: PDB / ID: 6aim | ||||||
---|---|---|---|---|---|---|---|
Title | Cab2 mutant H337A complex with phosphopantothenate-cysteine | ||||||
![]() | Phosphopantothenate--cysteine ligase CAB2 | ||||||
![]() | LIGASE / complex / Phosphopantothenate--cysteine | ||||||
Function / homology | ![]() CoA-synthesizing protein complex / Coenzyme A biosynthesis / phosphopantothenate-cysteine ligase (CTP) / phosphopantothenate--cysteine ligase activity / coenzyme A biosynthetic process / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zheng, P. / Zhu, Z. | ||||||
![]() | ![]() Title: Crystallographic Analysis of the Catalytic Mechanism of Phosphopantothenoylcysteine Synthetase from Saccharomyces cerevisiae. Authors: Zheng, P. / Zhang, M. / Khan, M.H. / Liu, H. / Jin, Y. / Yue, J. / Gao, Y. / Teng, M. / Zhu, Z. / Niu, L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 149.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 114.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 978.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 982.2 KB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 40.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ai8C ![]() 6ai9C ![]() 6aikC ![]() 6aipC ![]() 1p9oS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 42684.660 Da / Num. of mol.: 2 / Mutation: H337A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CAB2, YIL083C / Production host: ![]() ![]() References: UniProt: P40506, phosphopantothenate-cysteine ligase (CTP) #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.4 % |
---|---|
Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 200mM ammonium tartrate, 20% PEG 3350,2mM DTT, 2mM MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→56.78 Å / Num. obs: 40365 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.039 / Rrim(I) all: 0.099 / Net I/σ(I): 18.13 |
Reflection shell | Resolution: 2.04→2.09 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.596 / Num. unique obs: 2015 / Rpim(I) all: 0.269 / Rrim(I) all: 0.656 / % possible all: 99.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1P9O Resolution: 2.04→56.78 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.17 / 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: 121.97 Å2 / Biso mean: 42.428 Å2 / Biso min: 22.63 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.04→56.78 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.045→2.098 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|