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- PDB-8bv8: Crystal structure of the phage Mu protein Mom inactive mutant S124A -

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Basic information

Entry
Database: PDB / ID: 8bv8
TitleCrystal structure of the phage Mu protein Mom inactive mutant S124A
ComponentsMethylcarbamoylase mom
KeywordsVIRAL PROTEIN / Phage Mu Mom protein / N6-methylcarbamoyl-2'-deoxyadenosine / DNA hypermodification / glycyl-[tRNA(Gly)]
Function / homologysymbiont-mediated evasion of host restriction-modification system / : / transferase activity / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / metal ion binding / Methylcarbamoylase mom
Function and homology information
Biological speciesEscherichia phage Mu (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsSilva, 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
OrganizationGrant numberCountry
Foundation for Polish SciencePOIR.04.04.00-00-5D81/17-00 Poland
Polish National Science Centre2018/30/Q/NZ2/00669 Poland
Other governmentPolish National Agency for Academic Exchange PPI/APM/2018/1/00034
Other privateNew England Biolabs
CitationJournal: 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
DepositionDec 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylcarbamoylase mom
B: Methylcarbamoylase mom


Theoretical massNumber of molelcules
Total (without water)54,5152
Polymers54,5152
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-5 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.180, 66.480, 138.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Methylcarbamoylase mom / Adenine modification enzyme mom / Gene product 55 / gp55 / Gene product mom / gpMom / Modification of Mu / Mom


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 / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 3350, potassium thiocyanate, bis-tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.03→2.103 Å / Redundancy: 14 % / Num. unique obs: 3412 / CC1/2: 0.748 / CC star: 0.925 / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.20.1_4487phasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2447 1731 4.98 %
Rwork0.2147 33010 -
obs0.2162 34741 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.81 Å2
Refinement stepCycle: LAST / Resolution: 2.03→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3527 0 0 190 3717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00163639
X-RAY DIFFRACTIONf_angle_d0.434914
X-RAY DIFFRACTIONf_chiral_restr0.0391506
X-RAY DIFFRACTIONf_plane_restr0.0032630
X-RAY DIFFRACTIONf_dihedral_angle_d12.74011358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.090.42681410.42972707X-RAY DIFFRACTION99.51
2.09-2.160.43231400.35532679X-RAY DIFFRACTION99.51
2.16-2.240.32431420.30392706X-RAY DIFFRACTION99.27
2.24-2.320.29031390.26632692X-RAY DIFFRACTION99.51
2.32-2.430.29561430.25782734X-RAY DIFFRACTION99.79
2.43-2.560.31741440.2692730X-RAY DIFFRACTION99.72
2.56-2.720.32221420.29222726X-RAY DIFFRACTION99.65
2.72-2.930.32531450.23422742X-RAY DIFFRACTION99.83
2.93-3.220.29891450.2192755X-RAY DIFFRACTION100
3.22-3.690.23391460.19572776X-RAY DIFFRACTION99.97
3.69-4.650.16631480.16722812X-RAY DIFFRACTION99.97
4.65-47.940.21761560.19442951X-RAY DIFFRACTION99.87

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