+Open data
-Basic information
Entry | Database: PDB / ID: 6aik | ||||||
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Title | Cab2 mutant H337A complex with phosphopantothenoyl-CMP | ||||||
Components | Phosphopantothenate--cysteine ligase CAB2 | ||||||
Keywords | LIGASE / Phosphopantothenate--cysteine ligase / complex / phosphopantothenoyl-CMP | ||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Zheng, P. / Zhu, Z. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aik.cif.gz | 154.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aik.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 6aik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aik_validation.pdf.gz | 877.9 KB | Display | wwPDB validaton report |
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Full document | 6aik_full_validation.pdf.gz | 888.8 KB | Display | |
Data in XML | 6aik_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 6aik_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/6aik ftp://data.pdbj.org/pub/pdb/validation_reports/ai/6aik | HTTPS FTP |
-Related structure data
Related structure data | 6ai8C 6ai9C 6aimC 6aipC 1p9oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CAB2, YIL083C / Production host: Escherichia coli (E. coli) References: UniProt: P40506, phosphopantothenate-cysteine ligase (CTP) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.66 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 200mM potassium sodium tartrate 20% PEG3350 2mM MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→56.26 Å / Num. obs: 54950 / % possible obs: 98.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 29.04 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.041 / Rrim(I) all: 0.094 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.83→1.88 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.926 / Num. unique obs: 2714 / CC1/2: 0.711 / Rpim(I) all: 0.488 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P9O Resolution: 1.83→56.26 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.135 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: 98.91 Å2 / Biso mean: 36.699 Å2 / Biso min: 16.43 Å2
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Refinement step | Cycle: final / Resolution: 1.83→56.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.831→1.878 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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