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Open data
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Basic information
Entry | Database: PDB / ID: 6ai8 | ||||||
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Title | Cab2 mutant-H337A | ||||||
![]() | Phosphopantothenate--cysteine ligase CAB2 | ||||||
![]() | LIGASE / Phosphopantothenate--cysteine ligase | ||||||
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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.2 KB | Display | ![]() |
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PDB format | ![]() | 111.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.5 KB | Display | ![]() |
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Full document | ![]() | 465.7 KB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ai9C ![]() 6aikC ![]() 6aimC ![]() 6aipC ![]() 1p9oS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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 | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 40.22 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM HEPES pH7.0, 18% PEG 4000 and 150mM (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→57.685 Å / Num. obs: 30686 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.036 / Rrim(I) all: 0.085 / Net I/σ(I): 16.26 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1547 / CC1/2: 0.936 / Rpim(I) all: 0.196 / Rrim(I) all: 0.456 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1P9O Resolution: 2.3→57.68 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.745 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.246 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.48 Å2 / Biso mean: 63.992 Å2 / Biso min: 34.13 Å2
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Refinement step | Cycle: final / Resolution: 2.3→57.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.297→2.356 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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