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- PDB-4qji: Crystal Structure of the C-terminal CTP-binding domain of a Phosp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qji | ||||||
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Title | Crystal Structure of the C-terminal CTP-binding domain of a Phosphopantothenoylcysteine decarboxylase/phosphopantothenate-cysteine ligase with bound CTP from Mycobacterium smegmatis | ||||||
![]() | Phosphopantothenate--cysteine ligase | ||||||
![]() | LIGASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / DNA / pantothenate metabolism flavoprotein / CTP-binding / pantothenate metablosim | ||||||
Function / homology | ![]() pantothenate catabolic process / phosphopantothenoylcysteine decarboxylase / phosphopantothenate-cysteine ligase (CTP) / phosphopantothenate--cysteine ligase activity / phosphopantothenoylcysteine decarboxylase complex / phosphopantothenoylcysteine decarboxylase activity / coenzyme A biosynthetic process / FMN binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Crystal Structure of the C-terminal CTP-binding domain of a Phosphopantothenoylcysteine decarboxylase/phosphopantothenate-cysteine ligase with bound CTP from Mycobacterium smegmatis Authors: Dranow, D.M. / Abendroth, J. / Wernimont, A.K. / Edwards, T.E. / Lorimer, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.7 KB | Display | ![]() |
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PDB format | ![]() | 133 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: CTP / End label comp-ID: CTP / Auth seq-ID: 184 - 500 / Label seq-ID: 7
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Details | AUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN |
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Components
#1: Protein | Mass: 24773.990 Da / Num. of mol.: 2 / Fragment: unp residues 186-414 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0QWT2, phosphopantothenate-cysteine ligase (CTP) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.03 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Wiz3/4(f7): 25% PEG-1500, 0.1M MMT Buffer, pH=7.0; protein was incubated with 10mM each CTP and pantothenate, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2014 / Details: Beryllium Lenses | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→50 Å / Num. all: 14877 / Num. obs: 14512 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.41 Å2 / Rmerge(I) obs: 0.059 / Χ2: 0.966 / Net I/σ(I): 16.72 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 160.49 Å2 / Biso mean: 63.814 Å2 / Biso min: 26.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→33.11 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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