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- PDB-5ft0: Crystal structure of gp37(Dip) from bacteriophage phiKZ -

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Basic information

Entry
Database: PDB / ID: 5ft0
TitleCrystal structure of gp37(Dip) from bacteriophage phiKZ
ComponentsGP37
KeywordsHYDROLASE INHIBITOR / GP37 / DIP / PHIKZ / BACTERIOPHAGE / RNASE E / RIBONUCLEASE INHIBITOR / RNA DEGRADOSOME
Function / homologyGp37/Dip protein / gp37/Dip protein / ARGININE / : / PHIKZ037
Function and homology information
Biological speciesPSEUDOMONAS PHAGE PHIKZ (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsVan den Bossche, A. / Hardwick, S.W. / Ceyssens, P.J. / Hendrix, H. / Voet, M. / Dendooven, T. / Bandyra, K.J. / De Maeyer, M. / Aertsen, A. / Noben, J.P. ...Van den Bossche, A. / Hardwick, S.W. / Ceyssens, P.J. / Hendrix, H. / Voet, M. / Dendooven, T. / Bandyra, K.J. / De Maeyer, M. / Aertsen, A. / Noben, J.P. / Luisi, B.F. / Lavigne, R.
CitationJournal: Elife / Year: 2016
Title: Structural elucidation of a novel mechanism for the bacteriophage-based inhibition of the RNA degradosome.
Authors: Van den Bossche, A. / Hardwick, S.W. / Ceyssens, P.J. / Hendrix, H. / Voet, M. / Dendooven, T. / Bandyra, K.J. / De Maeyer, M. / Aertsen, A. / Noben, J.P. / Luisi, B.F. / Lavigne, R.
History
DepositionJan 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GP37
B: GP37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9746
Polymers64,5452
Non-polymers4294
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-19.9 kcal/mol
Surface area25360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.040, 65.020, 85.400
Angle α, β, γ (deg.)90.00, 107.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GP37 / PHIKZ037


Mass: 32272.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHIKZ (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q8SDC5
#2: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.99 Å3/Da / Density % sol: 58.85 % / Description: NONE
Crystal growDetails: 100 MM KH2PO4, 100 MM NAH2PO4, 100 MM MES PH 6.0, 800 MM NACL, 0.2 M SODIUM THIOCYANATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97851
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 2.2→68.6 Å / Num. obs: 38346 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXAUTOSOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.2→46.025 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 22.83 / Stereochemistry target values: ML
Details: UNKNOWN LIGAND CAUTIOUSLY MODELLED AS ARGININE CHAIN C
RfactorNum. reflection% reflection
Rfree0.2189 1925 5 %
Rwork0.1939 --
obs0.1952 38321 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 21 250 4281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044165
X-RAY DIFFRACTIONf_angle_d0.6555671
X-RAY DIFFRACTIONf_dihedral_angle_d12.6832473
X-RAY DIFFRACTIONf_chiral_restr0.049647
X-RAY DIFFRACTIONf_plane_restr0.003734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.32081480.27862588X-RAY DIFFRACTION100
2.255-2.3160.29511210.26152598X-RAY DIFFRACTION100
2.316-2.38410.28121200.25052583X-RAY DIFFRACTION100
2.3841-2.46110.27251400.24532566X-RAY DIFFRACTION100
2.4611-2.5490.29421160.22912628X-RAY DIFFRACTION100
2.549-2.65110.24851500.22512568X-RAY DIFFRACTION100
2.6511-2.77170.24951500.21832591X-RAY DIFFRACTION100
2.7717-2.91780.24491460.21342573X-RAY DIFFRACTION100
2.9178-3.10060.22521410.19782600X-RAY DIFFRACTION100
3.1006-3.340.22731250.18872607X-RAY DIFFRACTION100
3.34-3.67590.17211630.17132565X-RAY DIFFRACTION100
3.6759-4.20750.18841520.16372603X-RAY DIFFRACTION99
4.2075-5.29980.16831350.15452617X-RAY DIFFRACTION100
5.2998-46.03530.23121180.19532709X-RAY DIFFRACTION99

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