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- PDB-4oj6: Crystal Structure of a Putative Tailspike Protein (TSP1, orf210) ... -

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Basic information

Entry
Database: PDB / ID: 4oj6
TitleCrystal Structure of a Putative Tailspike Protein (TSP1, orf210) from Escherichia coli O157:H7 Bacteriohage CBA120; Se-Met Protein
ComponentsTailspike protein
KeywordsVIRAL PROTEIN / parallel beta helix / putative endo-glycosidase / bacterial polysaccharide / phage baseplate / phage tail
Function / homology
Function and homology information


biological process involved in interaction with host / viral life cycle / virion component
Similarity search - Function
Pectate Lyase C-like - #130 / Seminal Fluid Protein PDC-109 (Domain B) - #80 / NE0471 N-terminal domain-like - #50 / NE0471 N-terminal domain-like / Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Seminal Fluid Protein PDC-109 (Domain B) / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold ...Pectate Lyase C-like - #130 / Seminal Fluid Protein PDC-109 (Domain B) - #80 / NE0471 N-terminal domain-like - #50 / NE0471 N-terminal domain-like / Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Seminal Fluid Protein PDC-109 (Domain B) / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / 3 Solenoid / Ribbon / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia phage Cba120 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsChen, C. / Herzberg, O.
CitationJournal: 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.
History
DepositionJan 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tailspike protein
B: Tailspike protein
C: Tailspike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,3194
Polymers250,2543
Non-polymers651
Water42,5512362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20750 Å2
ΔGint-132 kcal/mol
Surface area72520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.299, 153.086, 171.444
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 Tailspike protein


Mass: 83417.852 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Cba120 (virus) / Gene: orf210 / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: G3M189
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2362 / 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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris pH 7.0-7.6, 20% PEG-1000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97945, 0.97961, 0.94945, 1.03320
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2012 / Details: mirrors
RadiationMonochromator: Si 1 1 1 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.979611
30.949451
41.03321
ReflectionResolution: 1.8→90 Å / Num. all: 298429 / Num. obs: 297461 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / Num. unique all: 21821 / Rsym value: 0.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AutoSolphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.851 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 22.18 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2095 14894 5.01 %random
Rwork0.187 ---
obs0.1881 297459 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→19.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16865 0 1 2362 19228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817174
X-RAY DIFFRACTIONf_angle_d1.13823358
X-RAY DIFFRACTIONf_dihedral_angle_d13.2386110
X-RAY DIFFRACTIONf_chiral_restr0.0762724
X-RAY DIFFRACTIONf_plane_restr0.0053026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82040.38454830.37129303X-RAY DIFFRACTION99
1.8204-1.84180.37754740.35769311X-RAY DIFFRACTION99
1.8418-1.86430.37044490.34269338X-RAY DIFFRACTION99
1.8643-1.88790.33945100.32829286X-RAY DIFFRACTION99
1.8879-1.91270.33364390.31339326X-RAY DIFFRACTION99
1.9127-1.93890.34155140.31779322X-RAY DIFFRACTION99
1.9389-1.96660.29454890.29229366X-RAY DIFFRACTION100
1.9666-1.99590.29954860.27549298X-RAY DIFFRACTION100
1.9959-2.0270.29855010.26299364X-RAY DIFFRACTION100
2.027-2.06020.27954820.25029353X-RAY DIFFRACTION100
2.0602-2.09570.28185030.23739364X-RAY DIFFRACTION100
2.0957-2.13380.26555190.23129366X-RAY DIFFRACTION100
2.1338-2.17480.24245170.21749335X-RAY DIFFRACTION100
2.1748-2.21910.22625090.21449345X-RAY DIFFRACTION100
2.2191-2.26730.25185020.22529363X-RAY DIFFRACTION100
2.2673-2.320.23724770.19829437X-RAY DIFFRACTION100
2.32-2.37790.21694840.18619377X-RAY DIFFRACTION100
2.3779-2.44210.2095140.18249407X-RAY DIFFRACTION100
2.4421-2.51380.22124940.18089451X-RAY DIFFRACTION100
2.5138-2.59480.20724980.17869398X-RAY DIFFRACTION100
2.5948-2.68730.21315030.17119436X-RAY DIFFRACTION100
2.6873-2.79460.19114830.16979440X-RAY DIFFRACTION100
2.7946-2.92140.19475070.17069440X-RAY DIFFRACTION100
2.9214-3.07490.19415080.1759483X-RAY DIFFRACTION100
3.0749-3.26680.19045340.17119448X-RAY DIFFRACTION100
3.2668-3.51770.18925280.16229489X-RAY DIFFRACTION100
3.5177-3.86940.16634960.14379518X-RAY DIFFRACTION100
3.8694-4.42390.14845050.13199595X-RAY DIFFRACTION100
4.4239-5.55330.13054830.11949672X-RAY DIFFRACTION100
5.5533-19.85220.16825030.15779934X-RAY DIFFRACTION100

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