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- PDB-2fsd: A Common Fold for the Receptor Binding Domains of Lactococcal Pha... -

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Basic information

Entry
Database: PDB / ID: 2fsd
TitleA Common Fold for the Receptor Binding Domains of Lactococcal Phages? The Crystal Structure of the Head Domain of Phage bIL170
Componentsputative baseplate protein
KeywordsVIRAL PROTEIN / Phage / Lactococcus lactis / receptor binding protein / head domain
Function / homology
Function and homology information


Phage bIL170 RBP, head domain / Phage bIL170 RBP, head domain / : / Lactophage receptor-binding protein N-terminal shoulder domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative baseplate protein
Similarity search - Component
Biological speciesunidentified phage (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsRicagno, S. / Cambillau, C.
CitationJournal: J.Virol. / Year: 2006
Title: Crystal Structure of the Receptor-Binding Protein Head Domain from Lactococcus lactis Phage bIL170
Authors: Ricagno, S. / Campanacci, V. / Blangy, S. / Spinelli, S. / Tremblay, D. / Moineau, S. / Tegoni, M. / Cambillau, C.
History
DepositionJan 22, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative baseplate protein
B: putative baseplate protein


Theoretical massNumber of molelcules
Total (without water)30,5682
Polymers30,5682
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.650, 69.650, 95.356
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a trimer. The crystal assymmetric unit contains a dimer

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Components

#1: Protein putative baseplate protein / RBP


Mass: 15284.188 Da / Num. of mol.: 2 / Fragment: RBP head domain, Residues 1-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified phage (virus) / Strain: bIL170 / Production host: Escherichia coli (E. coli) / References: UniProt: O80120
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: nanodrop setting (300 nL), pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.3→32.7 Å / Num. all: 12327 / Num. obs: 12327 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.42 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→23.8 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.86 / SU B: 7.333 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26801 606 4.9 %RANDOM
Rwork0.24176 ---
all0.24305 11702 --
obs0.24305 11702 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.229 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.08 Å2
Refine analyzeLuzzati coordinate error free: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 0 98 1708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221652
X-RAY DIFFRACTIONr_bond_other_d0.0010.021500
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9632266
X-RAY DIFFRACTIONr_angle_other_deg0.77933498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89924.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88215228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.955156
X-RAY DIFFRACTIONr_chiral_restr0.0710.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021862
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
X-RAY DIFFRACTIONr_nbd_refined0.1890.2292
X-RAY DIFFRACTIONr_nbd_other0.1810.21516
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2792
X-RAY DIFFRACTIONr_nbtor_other0.0860.2937
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.284
X-RAY DIFFRACTIONr_xyhbond_nbd_other00.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.210
X-RAY DIFFRACTIONr_mcbond_it0.6511.51383
X-RAY DIFFRACTIONr_mcbond_other0.0891.5446
X-RAY DIFFRACTIONr_mcangle_it0.77721784
X-RAY DIFFRACTIONr_scbond_it0.9573642
X-RAY DIFFRACTIONr_scangle_it1.3954.5482
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 52 -
Rwork0.255 837 -
obs--99.66 %

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