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- PDB-5e7f: Complex between lactococcal phage Tuc2009 RBP head domain and a n... -

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Basic information

Entry
Database: PDB / ID: 5e7f
TitleComplex between lactococcal phage Tuc2009 RBP head domain and a nanobody (L06)
Components
  • Major structural protein 1
  • nanobody L06
KeywordsVIRAL PROTEIN / bacteriophages / Lactococcus lactis / Siphoviridae / receptor binding protein / single-chain nanobody
Function / homologyLower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Major structural protein 1
Function and homology information
Biological speciesCamelus dromedarius (Arabian camel)
Lactococcus phage Tuc2009 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2May 4, 2016Group: Database references
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_strain
Revision 1.4Jan 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: nanobody L06
B: nanobody L06
C: nanobody L06
G: Major structural protein 1
H: Major structural protein 1
I: Major structural protein 1


Theoretical massNumber of molelcules
Total (without water)99,4316
Polymers99,4316
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-65 kcal/mol
Surface area31440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.730, 88.040, 147.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody nanobody L06


Mass: 14164.479 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: blood (immunization) / Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli BL21 (bacteria)
#2: Protein Major structural protein 1


Mass: 18979.213 Da / Num. of mol.: 3 / Fragment: head domain, UNP residues 1-173
Source method: isolated from a genetically manipulated source
Details: Cleaved by trypsin / Source: (gene. exp.) Lactococcus phage Tuc2009 (virus) / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: Q38610
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: mixing 300 nl of protein (10 mM HEPES, pH 7.5, 150 mM NaCl) with 100 nl precipitant solution (25-30 % PEG4000, 0.2 M Imidazole pH 6.0, or 0.1 M Tris pH 8.0).
PH range: 7.5 - 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.99 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.7→47.1 Å / Num. obs: 31023 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 75.17 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 11
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1.2 / % possible all: 99.9

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Processing

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

5efb


Resolution: 2.7→34.8 Å / Cor.coef. Fo:Fc: 0.8883 / Cor.coef. Fo:Fc free: 0.8783 / SU R Cruickshank DPI: 0.464 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.457 / SU Rfree Blow DPI: 0.24 / SU Rfree Cruickshank DPI: 0.244
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 1550 5 %RANDOM
Rwork0.1941 ---
obs0.1948 31009 99.93 %-
Displacement parametersBiso mean: 78.75 Å2
Baniso -1Baniso -2Baniso -3
1--15.5784 Å20 Å20 Å2
2---21.1031 Å20 Å2
3---36.6815 Å2
Refine analyzeLuzzati coordinate error obs: 0.395 Å
Refinement stepCycle: LAST / Resolution: 2.7→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5848 0 0 40 5888
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086009HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.028167HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1945SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes135HARMONIC2
X-RAY DIFFRACTIONt_gen_planes902HARMONIC5
X-RAY DIFFRACTIONt_it6009HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion18.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion776SEMIHARMONIC5
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_contact6765SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.79 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3565 140 4.98 %
Rwork0.2805 2672 -
all0.2841 2812 -
obs--99.86 %
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)
11.2811-0.39530.21451.8985-0.82615.67860.06780.08130.1017-0.1246-0.0673-0.03920.17070.2417-0.0005-0.0560.041-0.0407-0.09680.0594-0.0652-47.3605-22.102983.3477
23.6205-0.3522-0.63755.2314-0.02044.0052-0.00920.1529-0.4724-0.0675-0.0136-0.07390.66010.18750.02290.39170.09950.04640.0188-0.09580.0161-10.2613-51.847461.9274
32.831.1649-0.09172.30560.37674.4083-0.11930.20920.0671-0.22110.0215-0.1819-0.28170.15870.09790.06170.00810.0193-0.1783-0.0055-0.076-36.0561-69.671107.343
43.9059-0.29230.25432.4607-0.42233.53130.0465-0.0415-0.05470.113-0.03310.0027-0.23510.2767-0.01340.05460.02250.0643-0.13150.0463-0.1527-26.0304-35.7652104.255
50.9-0.8512-0.95971.62460.1555.66890.0694-0.13780.01470.1216-0.0402-0.1372-0.10280.3797-0.0292-0.033-0.05970.0643-0.02830.07190.0152-12.9847-32.238588.6179
62.62081.3586-0.32923.1066-0.28883.4421-0.0694-0.1718-0.32590.0114-0.1103-0.47340.43110.26650.17960.05420.18030.07990.04530.06690.0723-11.8926-50.061899.0792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ G|* }
5X-RAY DIFFRACTION5{ H|* }
6X-RAY DIFFRACTION6{ I|* }

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