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- PDB-4cry: Direct visualisation of strain-induced protein post-translational... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cry | ||||||
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Title | Direct visualisation of strain-induced protein post-translational modification | ||||||
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![]() | LYASE / COENZYME A / RADIATION DAMAGE / PANTOTHENATE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() Title: Direct Visualisation of Strain-Induced Protein Post-Translational Modification 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.7 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 686.4 KB | Display | ![]() |
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Full document | ![]() | 693.5 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4azdS 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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1 | ![]()
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Unit cell |
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Components
-Protein/peptide , 1 types, 1 molecules A
#1: Protein/peptide | Mass: 4770.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: RESIDUES 1-24 AFTER CLEAVAGE OF POLYPEPTIDE CHAIN BACKBONE BETWEEN RESIDUES G24 AND S25 Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Protein , 2 types, 2 molecules BG
#2: Protein | Mass: 15738.804 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#3: Protein | Mass: 11041.375 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: RESIDUES 25-126 AFTER CLEAVAGE OF POLYPEPTIDE CHAIN BACKBONE BETWEEN RESIDUES G24 AND S25 Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 127 molecules ![](data/chem/img/ACO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ACO / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-CL / |
#7: Water | ChemComp-HOH / |
-Details
Sequence details | N-TERMINAL HEXAHIS-TAGGED ADC. RESIDUES 1-24 RESIDUES 25-126, POINT MUTATION T57V. C-TERMINAL ...N-TERMINAL HEXAHIS-TAGGED ADC. RESIDUES 1-24 RESIDUES 25-126, POINT MUTATION T57V. C-TERMINAL HEXAHIS-TAGGED PANZ. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 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: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2013 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.61→59.1 Å / Num. obs: 37491 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.8 | |||||||||||||||
Reflection shell | Resolution: 1.61→1.64 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.6 / % possible all: 80.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4AZD Resolution: 1.61→43.19 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.916 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.013 / 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: 26.268 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→43.19 Å
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Refine LS restraints |
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