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- PDB-4a0t: Structure of the carboxy-terminal domain of bacteriophage T7 fibr... -

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Basic information

Entry
Database: PDB / ID: 4a0t
TitleStructure of the carboxy-terminal domain of bacteriophage T7 fibre gp17 containing residues 371-553.
ComponentsTAIL FIBER PROTEIN
KeywordsVIRAL PROTEIN / CAUDOVIRALES / PODOVIRIDAE / BETA-HELIX / BETA-SANDWICH
Function / homology
Function and homology information


virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell / virion attachment to host cell / identical protein binding
Similarity search - Function
mini-chromosome maintenance (MCM) complex, domain 2 - #30 / Ubiquitin Ligase Nedd4; Chain: W; - #20 / Glycosyl hydrolase fold / Glycosyl hydrolase fold - #10 / Ubiquitin Ligase Nedd4; Chain: W; / mini-chromosome maintenance (MCM) complex, domain 2 / : / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Tail fibre protein gp37 C terminal domain ...mini-chromosome maintenance (MCM) complex, domain 2 - #30 / Ubiquitin Ligase Nedd4; Chain: W; - #20 / Glycosyl hydrolase fold / Glycosyl hydrolase fold - #10 / Ubiquitin Ligase Nedd4; Chain: W; / mini-chromosome maintenance (MCM) complex, domain 2 / : / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Tail fibre protein gp37 C terminal domain / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein / Other non-globular / Special / Sandwich / Mainly Beta
Similarity search - Domain/homology
trimethylamine oxide / Tail fiber protein
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsGarcia-Doval, C. / van Raaij, M.J.
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2012
Title: Structure of the receptor-binding carboxy-terminal domain of bacteriophage T7 tail fibers.
Authors: Garcia-Doval, C. / van Raaij, M.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Crystallization of the C-Terminal Domain of the Bacteriophage T7 Fibre Protein Gp17.
Authors: Garcia-Doval, C. / van Raaij, M.J.
History
DepositionSep 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Other
Revision 1.2Jun 20, 2012Group: Other
Revision 1.3Dec 28, 2016Group: Database references / Other / Structure summary
Revision 1.4Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: TAIL FIBER PROTEIN
B: TAIL FIBER PROTEIN
C: TAIL FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6488
Polymers76,0623
Non-polymers5865
Water13,583754
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15600 Å2
ΔGint-90 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.240, 86.040, 118.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.30332, 0.8606, 0.40911), (-0.18018, -0.36979, 0.91148), (0.9357, -0.35018, 0.04289)-24.90204, 60.89195, -0.32665
2given(0.31135, -0.1859, 0.93193), (0.86352, -0.35406, -0.35913), (0.39672, 0.91656, 0.05029)19.02257, 43.07534, -45.33705
3given(0.31806, 0.86223, 0.39421), (-0.19249, -0.34842, 0.91736), (0.92832, -0.36766, 0.05515)-25.53312, 59.96021, 0.2122

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Components

#1: Protein TAIL FIBER PROTEIN / BACTERIOPHAGE T7 FIBRE GP17


Mass: 25354.057 Da / Num. of mol.: 3 / Fragment: C-TERMINAL REGION, RESIDUES 371-553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE T7 (virus) / Description: DNA OBTAINED FROM LABORATORY OF JL CARRASCOSA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03748
#2: Chemical ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H9NO
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPOLY-ETHYLENEGLYCOL MME 2000 (1PE): FRAGMENT ONLY VISIBLE IN CRYSTAL STRUCTURE
Sequence detailsEXPRESSED AND CRYSTALLISED PROTEIN CONTAINS EXPRESSION TAG.

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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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS-HCL (PH 8.5), 0.2 M TRIMETHYLAMINE N-OXIDE 20-25% (W/V) POLY-ETHYLENE GLYCOL MONOMETHYL ETHER 2000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.03839
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2011 / Details: BENT COLLIMATING MIRROR AND TOROID
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03839 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 50056 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 13.906 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.9→19.86 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.862 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.20035 2111 4.2 %THIN SHELLS
Rwork0.15451 ---
obs0.15652 47889 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.315 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 35 754 5115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214473
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.8896064
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2265545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.40623.947228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.65315681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4791524
X-RAY DIFFRACTIONr_chiral_restr0.1050.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023491
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.22081
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23038
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2653
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6871.52704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21324300
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.16331769
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3294.51764
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→2.002 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.218 293 -
Rwork0.187 6859 -
obs--100 %

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