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Yorodumi- PDB-8bv8: Crystal structure of the phage Mu protein Mom inactive mutant S124A -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bv8 | |||||||||||||||
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Title | Crystal structure of the phage Mu protein Mom inactive mutant S124A | |||||||||||||||
Components | Methylcarbamoylase mom | |||||||||||||||
Keywords | VIRAL PROTEIN / Phage Mu Mom protein / N6-methylcarbamoyl-2'-deoxyadenosine / DNA hypermodification / glycyl-[tRNA(Gly)] | |||||||||||||||
Function / homology | symbiont-mediated evasion of host restriction-modification system / transferase activity / host cell cytoplasm / metal ion binding / Methylcarbamoylase mom Function and homology information | |||||||||||||||
Biological species | Escherichia phage Mu (virus) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | |||||||||||||||
Authors | Silva, R.M.B. / Slyvka, A. / Lee, Y.J. / Guan, C. / Lund, S.R. / Raleigh, E.A. / Skowronek, K. / Bochtler, M. / Weigele, P.R. | |||||||||||||||
Funding support | Poland, 4items
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Citation | Journal: To Be Published Title: Crystal structure of the phage Mu protein Mom catalytic mutant S124A Authors: Silva, R.M.B. / Slyvka, A. / Lee, Y.J. / Guan, C. / Lund, S.R. / Raleigh, E.A. / Skowronek, K. / Bochtler, M. / Weigele, P.R. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bv8.cif.gz | 128.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bv8.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 8bv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/8bv8 ftp://data.pdbj.org/pub/pdb/validation_reports/bv/8bv8 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27257.270 Da / Num. of mol.: 2 / Mutation: S124A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage Mu (virus) / Gene: mom, Mup55 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06018 #2: 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: 2.41 Å3/Da / Density % sol: 49.02 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 3350, potassium thiocyanate, bis-tris propane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→47.94 Å / Num. obs: 34815 / % possible obs: 99.7 % / Redundancy: 13.4 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1861 / Rpim(I) all: 0.05248 / Rrim(I) all: 0.1935 / Net I/σ(I): 14.64 |
Reflection shell | Resolution: 2.03→2.103 Å / Redundancy: 14 % / Num. unique obs: 3412 / CC1/2: 0.748 / CC star: 0.925 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→47.94 Å / SU ML: 0.3338 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.6195 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→47.94 Å
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Refine LS restraints |
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LS refinement shell |
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