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- PDB-6nw9: CRYSTAL STRUCTURE OF A TAILSPIKE PROTEIN 3 (TSP3, ORF212) FROM ES... -

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Basic information

Entry
Database: PDB / ID: 6nw9
TitleCRYSTAL STRUCTURE OF A TAILSPIKE PROTEIN 3 (TSP3, ORF212) FROM ESCHERICHIA COLI O157:H7 BACTERIOPHAGE CBA120
ComponentsTailspike protein
KeywordsVIRAL PROTEIN / PARALLEL BETA HELIX / PUTATIVE ENDO-GLYCOSIDASE / BACTERIAL POLYSACCHARIDE / PHAGE TAIL / PHAGE CBA120
Function / homology
Function and homology information


biological process involved in interaction with host / viral life cycle / virion component / metal ion binding
Similarity search - Function
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 / Right handed beta helix domain / Right handed beta helix region / Periplasmic copper-binding protein (NosD) / Pectin lyase fold / Pectin lyase fold/virulence factor / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Tailspike protein
Similarity search - Component
Biological speciesEscherichia virus CBA120
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsGreenfield, J.Y. / Herzberg, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM110202 United States
Citation
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.
#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.
History
DepositionFeb 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)213,20998
Polymers206,1953
Non-polymers7,01595
Water32,9311828
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48340 Å2
ΔGint-99 kcal/mol
Surface area57680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.439, 66.770, 161.600
Angle α, β, γ (deg.)90.00, 103.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Tailspike protein


Mass: 68731.547 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus CBA120 / Gene: orf212 / Plasmid: PBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami / References: UniProt: G3M191

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Non-polymers , 10 types, 1923 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO3
#6: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1828 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 18% PEG 8000, 0.2M sodium chloride, 0.1M N-Cyclohexyl-2-aminoethanesulfonic acid (CHES)
PH range: 9.0-9.8

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97932 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 18, 2015 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.85→54.158 Å / Num. obs: 175535 / % possible obs: 99.69 % / Redundancy: 2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 17301 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.14_3228:)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→54.158 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.43
RfactorNum. reflection% reflection
Rfree0.1839 8672 4.94 %
Rwork0.1506 --
obs0.1523 175535 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→54.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14059 0 444 1828 16331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01214882
X-RAY DIFFRACTIONf_angle_d1.35720098
X-RAY DIFFRACTIONf_dihedral_angle_d4.33111519
X-RAY DIFFRACTIONf_chiral_restr0.0722215
X-RAY DIFFRACTIONf_plane_restr0.0082561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.23353100.20655468X-RAY DIFFRACTION99
1.871-1.8930.24242650.19555478X-RAY DIFFRACTION99
1.893-1.91610.23223040.1845476X-RAY DIFFRACTION99
1.9161-1.94040.21963050.17585507X-RAY DIFFRACTION99
1.9404-1.96590.21912780.17275577X-RAY DIFFRACTION100
1.9659-1.99280.22042910.16765495X-RAY DIFFRACTION99
1.9928-2.02130.20633030.16245520X-RAY DIFFRACTION100
2.0213-2.05150.1942780.15395487X-RAY DIFFRACTION100
2.0515-2.08350.18752870.15165564X-RAY DIFFRACTION100
2.0835-2.11770.20462840.15565510X-RAY DIFFRACTION100
2.1177-2.15420.18932620.15325630X-RAY DIFFRACTION100
2.1542-2.19340.17512500.14665543X-RAY DIFFRACTION100
2.1934-2.23560.17342880.14685535X-RAY DIFFRACTION100
2.2356-2.28120.20162950.15365539X-RAY DIFFRACTION100
2.2812-2.33080.17143090.15585497X-RAY DIFFRACTION100
2.3308-2.3850.19052980.15165589X-RAY DIFFRACTION100
2.385-2.44470.19273100.14685508X-RAY DIFFRACTION100
2.4447-2.51080.17862850.14925518X-RAY DIFFRACTION100
2.5108-2.58470.19722800.1495588X-RAY DIFFRACTION100
2.5847-2.66810.18412880.14835591X-RAY DIFFRACTION100
2.6681-2.76350.18062890.1425567X-RAY DIFFRACTION100
2.7635-2.87410.18143050.14445569X-RAY DIFFRACTION100
2.8741-3.00490.18513110.14925547X-RAY DIFFRACTION100
3.0049-3.16330.17873000.14535589X-RAY DIFFRACTION100
3.1633-3.36150.1772730.14515610X-RAY DIFFRACTION100
3.3615-3.62090.15622740.13635633X-RAY DIFFRACTION100
3.6209-3.98520.15712850.135632X-RAY DIFFRACTION100
3.9852-4.56170.16272880.12755630X-RAY DIFFRACTION100
4.5617-5.74620.1652950.14315655X-RAY DIFFRACTION100
5.7462-54.18140.18892820.18395811X-RAY DIFFRACTION99

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