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- PDB-5e7t: Structure of the tripod (BppUct-A-L) from the baseplate of bacter... -

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Basic information

Entry
Database: PDB / ID: 5e7t
TitleStructure of the tripod (BppUct-A-L) from the baseplate of bacteriophage Tuc2009
Components
  • (Major structural protein ...) x 2
  • (Minor structural protein ...) x 2
KeywordsVIRAL PROTEIN / bacteriophages / Lactococcus lactis / Siphoviridae / nanobody / receptor binding protein
Function / homology
Function and homology information


: / Minor structural protein 5-like, C-terminal domain / : / Major structural protein 1, jelly-roll domain / Baseplate upper protein, immunoglobulin like domain / Baseplate upper protein immunoglobulin like domain / BppU, N-terminal / BppU N-terminal domain / Lower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain ...: / Minor structural protein 5-like, C-terminal domain / : / Major structural protein 1, jelly-roll domain / Baseplate upper protein, immunoglobulin like domain / Baseplate upper protein immunoglobulin like domain / BppU, N-terminal / BppU N-terminal domain / Lower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain / : / BppA domain 1 / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Major structural protein 1 / Minor structural protein 5 / Minor structural protein 4
Similarity search - Component
Biological speciesLactococcus phage Tuc2009 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLegrand, P. / Collins, B. / Blangy, S. / Murphy, J. / Spinelli, S. / Gutierrez, C. / Richet, N. / Kellenberger, C. / Desmyter, A. / Mahony, J. ...Legrand, P. / Collins, B. / Blangy, S. / Murphy, J. / Spinelli, S. / Gutierrez, C. / Richet, N. / Kellenberger, C. / Desmyter, A. / Mahony, J. / van Sinderen, D. / Cambillau, C.
CitationJournal: Mbio / Year: 2016
Title: The Atomic Structure of the Phage Tuc2009 Baseplate Tripod Suggests that Host Recognition Involves Two Different Carbohydrate Binding Modules.
Authors: Legrand, P. / Collins, B. / Blangy, S. / Murphy, J. / Spinelli, S. / Gutierrez, C. / Richet, N. / Kellenberger, C. / Desmyter, A. / Mahony, J. / van Sinderen, D. / Cambillau, C.
History
DepositionOct 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Minor structural protein 4
B: Minor structural protein 5
G: Major structural protein 1
H: Major structural protein 1
I: Major structural protein 1
L: Major structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,32312
Polymers121,8036
Non-polymers5206
Water1,09961
1
A: Minor structural protein 4
B: Minor structural protein 5
G: Major structural protein 1
H: Major structural protein 1
I: Major structural protein 1
L: Major structural protein 1
hetero molecules

A: Minor structural protein 4
B: Minor structural protein 5
G: Major structural protein 1
H: Major structural protein 1
I: Major structural protein 1
L: Major structural protein 1
hetero molecules

A: Minor structural protein 4
B: Minor structural protein 5
G: Major structural protein 1
H: Major structural protein 1
I: Major structural protein 1
L: Major structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,97036
Polymers365,40918
Non-polymers1,56118
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Unit cell
Length a, b, c (Å)211.960, 211.960, 211.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11L-202-

SO4

21L-202-

SO4

31L-304-

HOH

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Components

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Minor structural protein ... , 2 types, 2 molecules AB

#1: Protein Minor structural protein 4


Mass: 14132.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage Tuc2009 (virus) / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: Q9AYV5
#2: Protein Minor structural protein 5


Mass: 31884.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage Tuc2009 (virus) / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: Q9AYV4

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Major structural protein ... , 2 types, 4 molecules GHIL

#3: Protein Major structural protein 1


Mass: 18848.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage Tuc2009 (virus) / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: Q38610
#4: Protein Major structural protein 1


Mass: 18979.213 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage Tuc2009 (virus) / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: Q38610

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Non-polymers , 3 types, 67 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: by mixing 300 nl of protein (Na2HPO4, 10 mM; KH2PO4, 1.8 mM [pH7.4]; NaCl, 137 mM; KCl, 2.7 mM) with 100 nl precipitant solution (2 M Ammonium Sulfate, 0.1 M Na Hepes [pH 7]).
PH range: 7.0 - 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.9→34.9 Å / Num. obs: 70164 / % possible obs: 99.8 % / Redundancy: 13.7 % / Biso Wilson estimate: 103.95 Å2 / Rmerge(I) obs: 0.187 / Net I/σ(I): 10.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.9 / Mean I/σ(I) obs: 1.25 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E7F RBP domain

5e7f


Resolution: 2.9→34.85 Å / Cor.coef. Fo:Fc: 0.9343 / Cor.coef. Fo:Fc free: 0.9233 / SU R Cruickshank DPI: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.278 / SU Rfree Blow DPI: 0.227 / SU Rfree Cruickshank DPI: 0.235
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 3508 5 %RANDOM
Rwork0.2143 ---
obs0.2155 70164 99.9 %-
Displacement parametersBiso mean: 104.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.423 Å
Refinement stepCycle: LAST / Resolution: 2.9→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8126 0 26 61 8213
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018334HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1811302HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2780SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes210HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1203HARMONIC5
X-RAY DIFFRACTIONt_it8334HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion20.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1111SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8949SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3171 255 5 %
Rwork0.2821 4848 -
all0.2838 5103 -
obs--99.1 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
100.34910.21670.87360.94452.6593-0.00580.14740.0347-0.11220.1005-0.2322-0.17220.3702-0.0947-0.12330.04-0.0123-0.0944-0.0458-0.0508-22.424360.397136.12
20.9535-0.45810.19082.66950.62070.71940.09090.0026-0.0014-0.077-0.0266-0.07370.06710.0189-0.0643-0.2023-0.02140.0918-0.0478-0.0698-0.172-22.450827.489513.8041
30.45670.9027-1.54771.6441-1.79972.11580.05530.20290.09230.51330.01140.63660.0231-0.6305-0.06670.1299-0.54410.2870.0289-0.0514-0.0194-53.077638.136999.7439
40.70770.833-2.00821.3805-1.95232.49020.0677-0.3263-0.34910.4554-0.33930.18540.33620.16920.27160.4117-0.680.1403-0.01460.1472-0.09-41.117134.0225104.917
51.16170.9299-2.06061.8561-1.23181.8066-0.16360.063-0.3560.3035-0.34930.73470.5191-0.22860.51290.0349-0.73170.3264-0.3099-0.0960.107-47.065626.809694.9896
61.7198-1.4199-0.2092.062-0.08322.94940.114-0.0040.2925-0.0191-0.115-0.0098-0.4385-0.09480.0010.0389-0.0253-0.0180.0407-0.0835-0.1066-6.395510.72271.2779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ G|* }
4X-RAY DIFFRACTION4{ H|* }
5X-RAY DIFFRACTION5{ I|* }
6X-RAY DIFFRACTION6{ L|* }

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