+Open data
-Basic information
Entry | Database: PDB / ID: 6aim | ||||||
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Title | Cab2 mutant H337A complex with phosphopantothenate-cysteine | ||||||
Components | Phosphopantothenate--cysteine ligase CAB2 | ||||||
Keywords | LIGASE / complex / Phosphopantothenate--cysteine | ||||||
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: 2.04 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 | 6aim.cif.gz | 149.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aim.ent.gz | 114.9 KB | Display | PDB format |
PDBx/mmJSON format | 6aim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aim_validation.pdf.gz | 978.2 KB | Display | wwPDB validaton report |
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Full document | 6aim_full_validation.pdf.gz | 982.2 KB | Display | |
Data in XML | 6aim_validation.xml.gz | 28 KB | Display | |
Data in CIF | 6aim_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/6aim ftp://data.pdbj.org/pub/pdb/validation_reports/ai/6aim | HTTPS FTP |
-Related structure data
Related structure data | 6ai8C 6ai9C 6aikC 6aipC 1p9oS C: citing same article (ref.) S: Starting model for refinement |
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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 (strain ATCC 204508 / S288c) (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: 1.96 Å3/Da / Density % sol: 37.4 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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
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Refinement step | Cycle: final / Resolution: 2.04→56.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.045→2.098 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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