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- PDB-4a0u: Structure of the carboxy-terminal domain of bacteriophage T7 fibr... -

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Basic information

Entry
Database: PDB / ID: 4a0u
TitleStructure of the carboxy-terminal domain of bacteriophage T7 fibre gp17 containing residues 371-553, C2221 crystal form.
ComponentsTAIL FIBER PROTEIN
KeywordsVIRAL PROTEIN / CAUDOVIRALES / PODOVIRIDAE / BACTERIOPHAGE FIBRE / RECEPTOR BINDING / 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
CARBONATE ION / Tail fiber protein
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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)76,2305
Polymers76,1103
Non-polymers1202
Water16,394910
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15910 Å2
ΔGint-91.8 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.320, 145.560, 172.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-2025-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.48291, -0.56807, -0.66641), (0.72016, 0.17531, -0.6713), (0.49817, -0.80409, 0.32444)-9.12826, 32.99765, 28.81963
2given(-0.48899, 0.71846, 0.49468), (-0.56466, 0.17154, -0.8073), (-0.66487, -0.67409, 0.3218)-42.58369, 12.21945, 6.9213
3given(-0.49379, -0.56445, -0.66149), (0.71548, 0.16862, -0.67798), (0.49422, -0.80806, 0.32059)-9.48266, 32.83963, 29.05417

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Components

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


Mass: 25370.078 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-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 910 / Source method: isolated from a natural source / Formula: H2O
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: 2.81 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7
Details: 10 MM TRIS-HCL, 0.2 M AMMONIUM CITRATE (PH 7.0), 20 % (W/V) POLY-ETHYLENE GLYCOL 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
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 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 58236 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 19.41 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A0T

4a0t


Resolution: 2→19.95 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.93 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.19675 2273 3.9 %THIN SHELLS
Rwork0.14946 ---
obs0.15135 55922 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: 19.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2--1.27 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4348 0 8 910 5266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214484
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.371.8846080
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3165552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.03423.974229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.88215686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2471524
X-RAY DIFFRACTIONr_chiral_restr0.10.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023531
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.22259
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23033
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2809
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6781.52722
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19524326
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.16731762
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3844.51754
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: 2→2.107 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.233 322 -
Rwork0.204 8023 -
obs--100 %

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