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- PDB-5fub: Crystal Structure of zebrafish Protein Arginine Methyltransferase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fub | ||||||
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Title | Crystal Structure of zebrafish Protein Arginine Methyltransferase 2 catalytic domain with SAH | ||||||
![]() | PROTEIN ARGININE METHYLTRANSFERASE 2 | ||||||
![]() | TRANSFERASE / S-ADENOSYL-L-CYSTEINE / S-ADENOSYL-L-HOMOCYSTEINE | ||||||
Function / homology | ![]() peptidyl-arginine methylation / protein-arginine N-methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cura, V. / Troffer-Charlier, N. / Marechal, N. / Bonnefond, L. / Cavarelli, J. | ||||||
![]() | ![]() Title: Structural studies of protein arginine methyltransferase 2 reveal its interactions with potential substrates and inhibitors. Authors: Cura, V. / Marechal, N. / Troffer-Charlier, N. / Strub, J.M. / van Haren, M.J. / Martin, N.I. / Cianferani, S. / Bonnefond, L. / Cavarelli, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.1 KB | Display | ![]() |
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PDB format | ![]() | 116.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5fulC ![]() 5fwaC ![]() 5fwdC ![]() 5g02C ![]() 5jmqC ![]() 5k8vC C: citing same article ( |
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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 , 1 types, 1 molecules A
#1: Protein | Mass: 38376.770 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, UNP RESIDUES 73-408 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 190 molecules ![](data/chem/img/SAH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SAH / | ||||
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#3: Chemical | ChemComp-MES / | ||||
#4: Chemical | ChemComp-CL / | ||||
#5: Chemical | #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
-Details
Sequence details | CRYSTALLIZ |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64 % / Description: STARTING MODEL GENERATED BY BALBES |
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Crystal grow | pH: 6 Details: 9% PEG 20000, 300MM NACL,100MM MES PH 6.0 AND FOR CRYO IS 10% PEG 20000, 300MM NACL,100MM MES PH 6.0, 15% ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.4 Å / Num. obs: 35917 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.997→38.405 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 22.6 / Stereochemistry target values: ML
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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 mean: 45.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.997→38.405 Å
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Refine LS restraints |
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LS refinement shell |
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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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