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Yorodumi- PDB-4crz: Direct visualisation of strain-induced protein prost-translationa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4crz | ||||||
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Title | Direct visualisation of strain-induced protein prost-translational modification | ||||||
Components |
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Keywords | LYASE / COENZYME A / RADIATION DAMAGE / PANTOTHENATE | ||||||
Function / homology | Function and homology information alanine biosynthetic process / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / acetyl-CoA binding / pantothenate biosynthetic process / zymogen activation / acyltransferase activity, transferring groups other than amino-acyl groups / protein autoprocessing / protein processing / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Monteiro, D.C.F. / Patel, V. / Bartlett, C.P. / Grant, T.D. / Nozaki, S. / Gowdy, J.A. / Snell, E.H. / Niki, H. / Pearson, A.R. / Webb, M.E. | ||||||
Citation | Journal: Chem.Biol. / Year: 2015 Title: The Structure of the Pand/Panz Protein Complex Reveals Negative Feedback Regulation of Pantothenate Biosynthesis by Coenzyme A. Authors: Monteiro, D.C. / Patel, V. / Bartlett, C.P. / Nozaki, S. / Grant, T.D. / Gowdy, J.A. / Thompson, G.S. / Kalverda, A.P. / Snell, E.H. / Niki, H. / Pearson, A.R. / Webb, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4crz.cif.gz | 73.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4crz.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 4crz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/4crz ftp://data.pdbj.org/pub/pdb/validation_reports/cr/4crz | HTTPS FTP |
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-Related structure data
Related structure data | 4cs0C 4azdS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 15793.928 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PRSETA-ADC(T57V) / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): MG1655 PAND-PANZ-(DE3) / References: UniProt: P0A790, aspartate 1-decarboxylase |
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#2: Protein | Mass: 15738.804 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PET28A-PANZ / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): MG1655 PAND-PANZ-(DE3) / References: UniProt: P37613 |
-Non-polymers , 4 types, 148 molecules
#3: Chemical | ChemComp-SCN / |
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#4: Chemical | ChemComp-ACO / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | HEXAHIS-TAGGED ADC. POINT MUTATION T57V. C-TERMINAL HEXAHIS-TAGGED PANZ. |
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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: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: 20% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 |
Detector | Type: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Dec 3, 2013 / Details: VARIMAX OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→33.7 Å / Num. obs: 32244 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AZD Resolution: 1.7→29.52 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.563 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE BIOLOGICALLY RELEVANT HETEROOCTAMER IS FORMED BY APPLICATION OF THE CRYSTALLOGRAPHIC 4-FOLD SYMMETRY AXIS TO THE ASYMMETRIC UNIT CELL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE BIOLOGICALLY RELEVANT HETEROOCTAMER IS FORMED BY APPLICATION OF THE CRYSTALLOGRAPHIC 4-FOLD SYMMETRY AXIS TO THE ASYMMETRIC UNIT CELL CONTENTS. EACH ASU CONTAINS ONE ADC PROTOMER AND ONE PANZ PROTOMER.
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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 mean: 23.383 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.52 Å
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Refine LS restraints |
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