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Open data
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Basic information
Entry | Database: PDB / ID: 4ads | ||||||
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Title | Crystal structure of plasmodial PLP synthase complex | ||||||
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![]() | TRANSFERASE/TRANSFERASE / TRANSFERASE-TRANSFERASE COMPLEX / PYRIDOXAL 5-PHOSPHATE BIOSYNTHESIS | ||||||
Function / homology | ![]() pyridoxine metabolic process / vitamin B6 biosynthetic process / glutaminase complex / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / response to singlet oxygen / pyridoxal phosphate biosynthetic process / glutaminase / glutaminase activity / glutamine metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guedez, G. / Sinning, I. / Tews, I. | ||||||
![]() | ![]() Title: Assembly of the Eukaryotic Plp-Synthase Complex from Plasmodium and Activation of the Pdx1 Enzyme. Authors: Guedez, G. / Hipp, K. / Windeisen, V. / Derrer, B. / Gengenbacher, M. / Boettcher, B. / Sinning, I. / Kappes, B. / Tews, I. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 980.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 542.8 KB | Display | ![]() |
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Full document | ![]() | 655.2 KB | Display | |
Data in XML | ![]() | 111.6 KB | Display | |
Data in CIF | ![]() | 144.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4adtC ![]() 4aduC ![]() 2abwS C: citing same article ( S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
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Components
#1: Protein | Mass: 30807.857 Da / Num. of mol.: 6 / Fragment: RESIDUES 3-282 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 24346.857 Da / Num. of mol.: 6 / Fragment: RESIDUES 3-219 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Plasmid: PET21-A / Production host: ![]() ![]() #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN G, HIS 196 TO ASN ENGINEERED RESIDUE IN CHAIN H, HIS 196 TO ASN ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 6.2 Details: 0.1 M NA/K PHOSPHATE-PHOSPHATE PH 6.2, 0.2 M NACL, 6% PEG 8000, 0.01 M L-GLUTAMINE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.62 Å / Relative weight: 1 |
Reflection | Resolution: 3.61→50 Å / Num. obs: 47666 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.41 |
Reflection shell | Resolution: 3.6→3.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.7 / % possible all: 64.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ABW Resolution: 3.61→50 Å / Cor.coef. Fo:Fc: 0.816 / Cor.coef. Fo:Fc free: 0.79 / SU B: 110.297 / SU ML: 0.726 / Cross valid method: THROUGHOUT / ESU R Free: 0.812 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.946 Å2
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Refinement step | Cycle: LAST / Resolution: 3.61→50 Å
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Refine LS restraints |
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