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- PDB-1zru: structure of the lactophage p2 receptor binding protein in comple... -

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Basic information

Entry
Database: PDB / ID: 1zru
Titlestructure of the lactophage p2 receptor binding protein in complex with glycerol
Componentslactophage p2 receptor binding protein
KeywordsVIRAL PROTEIN / 3 domains: BETA BARREL / BETA PRISM / BETA BARREL / Structural Genomics / Structural Proteomics in Europe / SPINE
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
Triple-stranded beta-helix / Phage fibre proteins / 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 ...Triple-stranded beta-helix / Phage fibre proteins / 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
Similarity search - Component
Biological speciesLactococcus lactis phage p2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsSpinelli, S. / Tremblay, D.M. / Tegoni, M. / Blangy, S. / Huyghe, C. / Desmyter, A. / Labrie, S. / de Haard, H. / Moineau, S. / Cambillau, C. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Bacteriol. / Year: 2006
Title: Receptor-binding protein of Lactococcus lactis phages: identification and characterization of the saccharide receptor-binding site.
Authors: Tremblay, D.M. / Tegoni, M. / Spinelli, S. / Campanacci, V. / Blangy, S. / Huyghe, C. / Desmyter, A. / Labrie, S. / Moineau, S. / Cambillau, C.
History
DepositionMay 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lactophage p2 receptor binding protein
B: lactophage p2 receptor binding protein
C: lactophage p2 receptor binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5579
Polymers86,0043
Non-polymers5536
Water20,6091144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14360 Å2
ΔGint-72 kcal/mol
Surface area28790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.106, 92.057, 145.725
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: Protein lactophage p2 receptor binding protein


Mass: 28668.057 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis phage p2 (virus) / Species: Lactococcus phage 936 sensu lato / Gene: ORF 18 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: Q71AW2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1144 / 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: 3.05 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2005
RadiationMonochromator: diamond crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.73→40.56 Å / Num. all: 111507 / Num. obs: 110279 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 19.4 Å2
Reflection shellResolution: 1.73→1.77 Å / % possible all: 89.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BSD

2bsd


Resolution: 1.73→40.56 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.541 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19689 1106 1 %RANDOM
Rwork0.17527 ---
obs0.17547 110279 97.34 %-
all-110279 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.694 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.086 Å
Refinement stepCycle: LAST / Resolution: 1.73→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5780 0 36 1144 6960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225915
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.9338039
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5445752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19925.059255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40615953
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6231527
X-RAY DIFFRACTIONr_chiral_restr0.0930.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024421
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.22748
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24052
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2929
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8331.53834
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35626072
X-RAY DIFFRACTIONr_scbond_it2.18932371
X-RAY DIFFRACTIONr_scangle_it3.3414.51967
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.729→1.774 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 71 -
Rwork0.237 7450 -
obs--89.91 %
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)
10.0407-0.010.05560.21550.110.1477-0.00930.01320.0057-0.02210.0043-0.0272-0.0186-0.0220.0049-0.0177-0.00040.00810.0038-0.0052-0.004416.404347.932748.4772
20.20740.1480.05310.14950.07090.03830.0154-0.0288-0.0314-0.0036-0.0147-0.03980.02140.0132-0.00070.0058-0.00130.0019-0.01180.0047-0.003229.490936.264255.623
30.05920.09190.05640.15330.14110.3205-0.0112-0.0139-0.01680.0032-0.0038-0.0015-0.0098-0.02640.015-0.01840.0103-0.0138-0.0137-0.00160.015113.238939.527264.9936
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2642 - 264
2X-RAY DIFFRACTION2BB2 - 2642 - 264
3X-RAY DIFFRACTION3CC2 - 2642 - 264

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