+Open data
-Basic information
Entry | Database: PDB / ID: 4adt | ||||||
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Title | Crystal structure of plasmodial PLP synthase | ||||||
Components | PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE | ||||||
Keywords | TRANSFERASE / PYRIDOXAL 5-PHOSPHATE BIOSYNTHESIS | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / PHOSPHATE ION / : Function and homology information | ||||||
Biological species | PLASMODIUM BERGHEI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||
Authors | Guedez, G. / Sinning, I. / Tews, I. | ||||||
Citation | Journal: Structure / Year: 2012 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4adt.cif.gz | 114.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4adt.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 4adt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4adt_validation.pdf.gz | 448.9 KB | Display | wwPDB validaton report |
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Full document | 4adt_full_validation.pdf.gz | 455 KB | Display | |
Data in XML | 4adt_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 4adt_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/4adt ftp://data.pdbj.org/pub/pdb/validation_reports/ad/4adt | HTTPS FTP |
-Related structure data
Related structure data | 4adsC 4aduC 2nv2S 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: 32733.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM BERGHEI (eukaryote) / Strain: NK65 / Plasmid: PET21-A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q4Z0E8 #2: Chemical | ChemComp-PO4 / #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: 2.42 Å3/Da / Density % sol: 49.3 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→50 Å / Num. obs: 24370 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 46.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.42→2.46 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.1 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NV2 Resolution: 2.42→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 16.383 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.379 Å2
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Refinement step | Cycle: LAST / Resolution: 2.42→50 Å
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Refine LS restraints |
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