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- PDB-6w4q: Crystal structure of full-length tailspike protein 2 (TSP2, ORF21... -

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Basic information

Entry
Database: PDB / ID: 6w4q
TitleCrystal structure of full-length tailspike protein 2 (TSP2, ORF211) ) from Escherichia coli O157:H7 bacteriophage CAB120
ComponentsTail fiber
KeywordsHYDROLASE / glycosidase / tailspike protein / phage CBA120 / lipopolysaccharide degradation
Function / homologymetal ion binding / CARBONATE ION / Putative tail fiber
Function and homology information
Biological speciesEscherichia virus CBA120
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsGreenfield, J. / Herzberg, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM110202 United States
Citation
Journal: Sci Rep / Year: 2020
Title: Structure and function of bacteriophage CBA120 ORF211 (TSP2), the determinant of phage specificity towards E. coli O157:H7.
Authors: Greenfield, J. / Shang, X. / Luo, H. / Zhou, Y. / Linden, S.B. / Heselpoth, R.D. / Leiman, P.G. / Nelson, D.C. / Herzberg, O.
#1: Journal: PloS One / Year: 2014
Title: Crystal structure of ORF210 from E. coli O157:H1 phage CBA120 (TSP1), a putative tailspike protein
Authors: Chen, C. / Bales, P. / Greenfield, J. / Heselpoth, R.D. / Nelson, D.C. / Herzberg, O.
#2: Journal: Sci Rep / Year: 2019
Title: Structure and tailspike glycosidase machinery of ORF212 from E. coli O157:H7 phage CBA120 (TSP3).
Authors: Greenfield, J. / Shang, X. / Luo, H. / Zhou, Y. / Heselpoth, R.D. / Nelson, D.C. / Herzberg, O.
History
DepositionMar 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Tail fiber
B: Tail fiber
C: Tail fiber
D: Tail fiber
E: Tail fiber
F: Tail fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)605,028123
Polymers594,7656
Non-polymers10,263117
Water70,0243887
1
A: Tail fiber
B: Tail fiber
C: Tail fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,85388
Polymers297,3823
Non-polymers7,47185
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Tail fiber
E: Tail fiber
F: Tail fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,17535
Polymers297,3823
Non-polymers2,79332
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.992, 259.009, 269.696
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Tail fiber


Mass: 99127.453 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus CBA120 / Gene: orf211 / Plasmid: PBAD24
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): rosetta-gami 2 / Variant (production host): DE3 / References: UniProt: G3M190

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Non-polymers , 6 types, 4004 molecules

#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 78 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3887 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.8 M ammonium sulfate and 0.1M HEPES (pH 7.0) / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2015
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.85→48.36 Å / Num. obs: 491364 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 32.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Χ2: 1 / Net I/σ(I): 7.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5 % / Rmerge(I) obs: 2.17 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 24214 / Χ2: 1 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5w6p

5w6p


Resolution: 1.9→48.36 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.593 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.109 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1877 23018 5.1 %RANDOM
Rwork0.1668 ---
obs0.1679 430672 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.27 Å2 / Biso mean: 36.863 Å2 / Biso min: 14.61 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å20 Å2
2---0.93 Å20 Å2
3----1.08 Å2
Refinement stepCycle: final / Resolution: 1.9→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33887 0 628 3887 38402
Biso mean--59.44 45.61 -
Num. residues----4533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01235286
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.62347974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.60154617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01224.0271634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.729155415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.52315132
X-RAY DIFFRACTIONr_chiral_restr0.120.24806
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0226759
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 1690 -
Rwork0.319 31614 -
all-33304 -
obs--99.97 %

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