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- PDB-3da0: Crystal structure of a cleaved form of a chimeric receptor bindin... -

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Basic information

Entry
Database: PDB / ID: 3da0
TitleCrystal structure of a cleaved form of a chimeric receptor binding protein from Lactococcal phages subspecies TP901-1 and p2
ComponentsCleaved chimeric receptor binding protein from bacteriophages TP901-1 and p2
KeywordsVIRAL PROTEIN / lactococcal phage p2 / lactococcal phage TP901-1 receptor binding protein
Function / homology
Function and homology information


virus tail, baseplate / entry receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Lower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain / Phage tail base-plate Siphoviridae RBP, head domain / : / : / Lactophage receptor-binding protein N-terminal shoulder domain / Lactococcus phage p2, Receptor binding protein, neck domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain / Adenovirus pIV-like, attachment domain ...Lower baseplate protein, N-terminal / Lower baseplate protein N-terminal domain / Phage tail base-plate Siphoviridae RBP, head domain / : / : / Lactophage receptor-binding protein N-terminal shoulder domain / Lactococcus phage p2, Receptor binding protein, neck domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain / Adenovirus pIV-like, attachment domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor binding protein / BPP
Similarity search - Component
Biological speciesLactococcus phage TP901-1 (virus)
Lactococcus phage p2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.65 Å
AuthorsSiponen, M.I. / Blangy, S. / Spinelli, S. / Vera, L. / Cambillau, C. / Campanacci, V.
CitationJournal: J.Bacteriol. / Year: 2009
Title: Crystal structure of a chimeric receptor binding protein constructed from two lactococcal phages.
Authors: Siponen, M. / Spinelli, S. / Blangy, S. / Moineau, S. / Cambillau, C. / Campanacci, V.
History
DepositionMay 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref / struct_ref_seq_dif
Item: _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: 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: Cleaved chimeric receptor binding protein from bacteriophages TP901-1 and p2
B: Cleaved chimeric receptor binding protein from bacteriophages TP901-1 and p2
C: Cleaved chimeric receptor binding protein from bacteriophages TP901-1 and p2


Theoretical massNumber of molelcules
Total (without water)44,5313
Polymers44,5313
Non-polymers00
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-42.6 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.168, 43.682, 78.946
Angle α, β, γ (deg.)90.00, 101.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cleaved chimeric receptor binding protein from bacteriophages TP901-1 and p2


Mass: 14843.647 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage TP901-1 (virus), (gene. exp.) Lactococcus phage p2 (virus)
Gene: bpp, rbp / Plasmid: pDEST17 O/I / Production host: Escherichia coli (E. coli) / Strain (production host): C41 pLysRos / References: UniProt: Q9G096, UniProt: Q71AW2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 1.75991 Å3/Da / Density % sol: 30.110064 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 0.1M Imidazole-malate, 17% PEG4000, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2007 / Details: tiroidal mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.65→39.01 Å / Num. all: 48882 / Num. obs: 48882 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.166 / Rsym value: 0.166 / Net I/σ(I): 7.7
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6921 / Rsym value: 0.394 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR
Starting model: PDB entry 2bsd

2bsd


Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.542 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20149 1164 2.6 %RANDOM
Rwork0.16411 ---
all0.16505 44350 --
obs0.16505 44350 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.527 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.73 Å2
2---0.4 Å20 Å2
3---0.07 Å2
Refine analyzeLuzzati coordinate error free: 0.095 Å
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3080 0 0 303 3383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223199
X-RAY DIFFRACTIONr_bond_other_d0.0070.022102
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.9114362
X-RAY DIFFRACTIONr_angle_other_deg0.86235140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5345411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47724.621145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9515510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6891515
X-RAY DIFFRACTIONr_chiral_restr0.1010.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023635
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02652
X-RAY DIFFRACTIONr_nbd_refined0.190.2555
X-RAY DIFFRACTIONr_nbd_other0.2140.22317
X-RAY DIFFRACTIONr_nbtor_refined0.180.21630
X-RAY DIFFRACTIONr_nbtor_other0.0860.21853
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.219
X-RAY DIFFRACTIONr_mcbond_it1.6671.52511
X-RAY DIFFRACTIONr_mcbond_other0.3271.5836
X-RAY DIFFRACTIONr_mcangle_it1.65923239
X-RAY DIFFRACTIONr_scbond_it3.09331406
X-RAY DIFFRACTIONr_scangle_it4.1814.51118
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 86 -
Rwork0.202 3327 -
obs-86 99.97 %
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)
11.3397-0.1991-0.39720.45020.08330.64960.04140.25340.0659-0.0972-0.05120.1718-0.0447-0.11150.0098-0.05330.0126-0.0228-0.0034-0.0053-0.01916.3385.17615.521
20.3392-0.0380.10910.79390.07480.3617-0.01690.0763-0.11810.0129-0.01880.18170.09550.01040.0357-0.0444-0.01390.0131-0.038-0.0155-0.000411.814-9.93122.223
30.4403-0.13-0.10110.39640.20670.8063-0.02450.01570.04220.0428-0.00610.0551-0.01870.0640.0306-0.0261-0.00730.0153-0.03430.0081-0.030617.2875.01928.95
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA35 - 10435 - 104
2X-RAY DIFFRACTION1AA105 - 165105 - 165
3X-RAY DIFFRACTION2BB35 - 10535 - 105
4X-RAY DIFFRACTION2BB106 - 165106 - 165
5X-RAY DIFFRACTION3CC34 - 5934 - 59
6X-RAY DIFFRACTION3CC60 - 10460 - 104
7X-RAY DIFFRACTION3CC105 - 165105 - 165

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