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Open data
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Basic information
Entry | Database: PDB / ID: 6umq | ||||||
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Title | Structure of DUF89 | ||||||
![]() | Damage-control phosphatase DUF89 | ||||||
![]() | TRANSFERASE / Metabolite repair / DUF89 | ||||||
Function / homology | ![]() protein carboxyl O-methyltransferase activity / : / protein-glutamate O-methyltransferase activity / fructose-1-phosphatase activity / fructose 6-phosphate aldolase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / S-adenosylmethionine-dependent methyltransferase activity / phosphatase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation ...protein carboxyl O-methyltransferase activity / : / protein-glutamate O-methyltransferase activity / fructose-1-phosphatase activity / fructose 6-phosphate aldolase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / S-adenosylmethionine-dependent methyltransferase activity / phosphatase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / DNA damage response / enzyme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Perry, J.J. / Kenjic, N. / Dennis, T.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Human ARMT1 structure and substrate specificity indicates that it is a DUF89 family damage-control phosphatase. Authors: Dennis, T.N. / Kenjic, N. / Kang, A.S. / Lowenson, J.D. / Kirkwood, J.S. / Clarke, S.G. / Perry, J.J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 211.4 KB | Display | ![]() |
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PDB format | ![]() | 152.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 252.1 KB | Display | ![]() |
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Full document | ![]() | 252 KB | Display | |
Data in XML | ![]() | 1.2 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6umrC ![]() 3pt1S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51231.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9H993, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.64 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 18% PEG 4000, 200mM MgCl2, 100mM Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→66.49 Å / Num. obs: 85552 / % possible obs: 98.54 % / Redundancy: 6.1 % / Biso Wilson estimate: 14.26 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.85→1.916 Å / Rmerge(I) obs: 0.215 / Num. unique obs: 8480 / % possible all: 99.27 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PT1 Resolution: 1.85→66.49 Å / SU ML: 0.1745 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.4558 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 16.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→66.49 Å
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Refine LS restraints |
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LS refinement shell |
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