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- PDB-5ft1: Crystal structure of gp37(Dip) from bacteriophage phiKZ bound to ... -

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Basic information

Entry
Database: PDB / ID: 5ft1
TitleCrystal structure of gp37(Dip) from bacteriophage phiKZ bound to RNase E of Pseudomonas aeruginosa
Components
  • GP37
  • RIBONUCLEASE E
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / DIP / PHIKZ / BACTERIOPHAGE / RNASE E / RIBONUCLEASE INHIBITOR / RNA DEGRADOSOME / PSEUDOMONAS AERUGINOSA
Function / homology
Function and homology information


ribonuclease E / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / tRNA binding / rRNA binding ...ribonuclease E / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / tRNA binding / rRNA binding / magnesium ion binding / zinc ion binding / cytoplasm
Similarity search - Function
Gp37/Dip protein / gp37/Dip protein / Ribonuclease E/G / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E / Ribonuclease E/G family / RNA-binding domain, S1 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain ...Gp37/Dip protein / gp37/Dip protein / Ribonuclease E/G / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E / Ribonuclease E/G family / RNA-binding domain, S1 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
PHIKZ037 / Ribonuclease E
Similarity search - Component
Biological speciesPSEUDOMONAS PHAGE PHIKZ (virus)
PSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GP37
B: GP37
C: RIBONUCLEASE E
D: RIBONUCLEASE E
E: GP37
F: RIBONUCLEASE E
G: GP37
H: RIBONUCLEASE E
I: GP37
J: RIBONUCLEASE E
K: GP37
L: RIBONUCLEASE E


Theoretical massNumber of molelcules
Total (without water)208,17212
Polymers208,17212
Non-polymers00
Water181
1
A: GP37
C: RIBONUCLEASE E
E: GP37
F: RIBONUCLEASE E


Theoretical massNumber of molelcules
Total (without water)69,3914
Polymers69,3914
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-26.4 kcal/mol
Surface area32390 Å2
MethodPQS
2
B: GP37
D: RIBONUCLEASE E
G: GP37
H: RIBONUCLEASE E


Theoretical massNumber of molelcules
Total (without water)69,3914
Polymers69,3914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-27.2 kcal/mol
Surface area32050 Å2
MethodPQS
3
I: GP37
J: RIBONUCLEASE E
K: GP37
L: RIBONUCLEASE E


Theoretical massNumber of molelcules
Total (without water)69,3914
Polymers69,3914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-23.2 kcal/mol
Surface area32230 Å2
MethodPQS
Unit cell
Length a, b, c (Å)84.610, 84.650, 84.600
Angle α, β, γ (deg.)107.86, 107.88, 107.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
GP37 / PHIKZ037


Mass: 31991.303 Da / Num. of mol.: 6
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: Protein/peptide
RIBONUCLEASE E / / RNASE E


Mass: 2704.057 Da / Num. of mol.: 6 / Fragment: RESIDUES 756-775 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: Q9HZM8, ribonuclease E
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Description: DATA PROCESSED IN LOW SYMMETRY P1 SPACE GROUP AS REFINEMENT STATISTICS AND ELECTRON DENSITY FOR BOUND PEPTIDE WERE MARGINALLY BETTER THAN IN RECOMMENDED H32 SPACE GROUP
Crystal growDetails: 100 MM KH2PO4, 100 MM NAH2PO4, 100 MM MES PH 6.0, 300 MM NACL, 0.2 M SODIUM THIOCYANATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twinOperator: -L,-K,-H / Fraction: 0.5
ReflectionResolution: 2.75→72.2 Å / Num. obs: 39553 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.3
Reflection shellResolution: 2.75→2.84 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.7 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FT0

5ft0


Resolution: 2.75→72.188 Å / σ(F): 1.98 / Phase error: 32.82 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2934 2305 5.8 %
Rwork0.2629 --
obs0.266 39553 79.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→72.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11560 0 0 1 11561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411817
X-RAY DIFFRACTIONf_angle_d0.70916094
X-RAY DIFFRACTIONf_dihedral_angle_d14.56929
X-RAY DIFFRACTIONf_chiral_restr0.051852
X-RAY DIFFRACTIONf_plane_restr0.0062082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7508-2.81460.3668800.38141384X-RAY DIFFRACTION42
2.8146-2.88490.34331000.35681612X-RAY DIFFRACTION49
2.8849-2.96270.3921490.36981724X-RAY DIFFRACTION53
2.9627-3.04970.32841450.36561919X-RAY DIFFRACTION58
3.0497-3.14790.32441050.36892260X-RAY DIFFRACTION66
3.1479-3.26010.48711000.33382375X-RAY DIFFRACTION73
3.2601-3.39020.2731040.34562604X-RAY DIFFRACTION80
3.3902-3.5440.38421750.33862782X-RAY DIFFRACTION84
3.544-3.730.37682040.29792912X-RAY DIFFRACTION89
3.73-3.96260.27651120.28062983X-RAY DIFFRACTION91
3.9626-4.26670.29971560.26152931X-RAY DIFFRACTION89
4.2667-4.69260.27241810.2213007X-RAY DIFFRACTION90
4.6926-5.36390.20721860.23032912X-RAY DIFFRACTION90
5.3639-6.72860.4781580.27623059X-RAY DIFFRACTION93
6.7286-22.71250.2581950.20982929X-RAY DIFFRACTION88

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