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- PDB-2xgf: Structure of the bacteriophage T4 long tail fibre needle-shaped r... -

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Basic information

Entry
Database: PDB / ID: 2xgf
TitleStructure of the bacteriophage T4 long tail fibre needle-shaped receptor-binding tip
ComponentsLONG TAIL FIBER PROTEIN P37
KeywordsVIRAL PROTEIN / FIBER PROTEIN
Function / homology
Function and homology information


virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell / structural molecule activity
Similarity search - Function
heat- and protease-stable fragment of the bacteriophage t4 short fibre, domain 3 / Phage tail collar domain / Bacteriophage lambda, Tail fiber protein, repeat-1 / Phage tail fibre repeat / Phage tail collar domain superfamily / Phage tail collar domain / : / Phage Tail Collar Domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / : / Long-tail fiber protein gp37
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsBartual, S.G. / Otero, J.M. / Garcia-Doval, C. / Llamas-Saiz, A.L. / Kahn, R. / Fox, G.C. / van Raaij, M.J.
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2010
Title: Structure of the bacteriophage T4 long tail fiber receptor-binding tip.
Authors: Bartual, S.G. / Otero, J.M. / Garcia-Doval, C. / Llamas-Saiz, A.L. / Kahn, R. / Fox, G.C. / van Raaij, M.J.
#1: Journal: Protein Expr.Purif. / Year: 2010
Title: Two-Chaperone Assisted Soluble Expression and Purification of the Bacteriophage T4 Long Tail Fibre Protein Gp37.
Authors: Bartual, S.G. / Garcia-Doval, C. / Alonso, J. / Schoehn, G. / van Raaij, M.J.
History
DepositionJun 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Data collection / Version format compliance
Revision 1.2Feb 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 1.3May 8, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: LONG TAIL FIBER PROTEIN P37
B: LONG TAIL FIBER PROTEIN P37
C: LONG TAIL FIBER PROTEIN P37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,43911
Polymers73,9883
Non-polymers4518
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39500 Å2
ΔGint-208.2 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.340, 53.980, 112.750
Angle α, β, γ (deg.)90.00, 100.43, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 811 - 1026 / Label seq-ID: 27 - 242

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

NCS oper:
IDCodeMatrixVector
1given(-0.36879, 0.80308, 0.46803), (-0.80384, -0.52838, 0.27324), (0.46673, -0.27545, 0.84041)44.88408, 22.01918, -15.19804
2given(-0.34894, -0.81645, 0.46006), (0.81488, -0.50679, -0.28132), (0.46284, 0.27673, 0.84214)40.72417, -28.71368, -13.87851
3given(-0.27785, 0.85619, 0.43558), (-0.85817, -0.425, 0.28797), (0.43168, -0.29379, 0.85284)42.27775, 24.40421, -14.30125
4given(-0.36879, -0.80384, 0.46673), (0.80308, -0.52838, -0.27545), (0.46803, 0.27324, 0.84041)41.34594, -28.5976, -14.25117
5given(-0.34893, 0.81488, 0.46284), (-0.81645, -0.50679, 0.27673), (0.46006, -0.28132, 0.84214)44.0317, 22.53805, -15.12588
6given(-0.27785, -0.85817, 0.43168), (0.85619, -0.425, -0.29379), (0.43558, 0.28797, 0.85284)38.86351, -30.02766, -13.24638

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Components

#1: Protein LONG TAIL FIBER PROTEIN P37 / RECEPTOR-RECOGNIZING PROTEIN / PROTEIN GP37


Mass: 24662.695 Da / Num. of mol.: 3 / Fragment: DOMAINS 10 AND 11, RESIDUES 785-1026
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE T4 (virus)
Description: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN (DSMZ, BRAUNSCHWEIG, GERMANY), CATALOGUE NUMER 4505 (NCIMB 10360)
Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) / Variant (production host): PET(AP)G57, PCDF(SM)G38 / References: UniProt: P03744
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / 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: 3.19 Å3/Da / Density % sol: 62.42 % / Description: NONE
Crystal growpH: 5
Details: 10 MM HEPES-NAOH PH 7.5, 1 MM MANGANOUS CHLORIDE, 5 % (W/V) POLY-ETHYLENEGLYCOL 6000, 0.1 M SODIUM CITRATE PH 5.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONESRF ID23-210.8726
SYNCHROTRONESRF ID23-121.73945, 1.74115
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDFeb 14, 2010PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY
ADSC CCD2CCDFeb 14, 2010PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTALSINGLE WAVELENGTHMx-ray1
2HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTALMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.87261
21.739451
31.741151
ReflectionResolution: 2.2→22 Å / Num. obs: 47653 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

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Processing

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

Resolution: 2.2→22 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.935 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WERE REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23813 2028 4.3 %THIN SHELLS
Rwork0.17933 ---
obs0.18184 45619 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.542 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å2-0.5 Å2
2---0.58 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.2→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4656 0 11 665 5332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214779
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9066498
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.025645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93223.667180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03415657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8051512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213706
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1730.21898
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.23170
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2445
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6771.53180
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29725061
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.23931599
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6594.51437
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 1552 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional1.255
2Bloose positional1.25
3Cloose positional1.235
1Aloose thermal2.3610
2Bloose thermal2.3510
3Cloose thermal2.4710
LS refinement shellResolution: 2.2→2.318 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.292 226 -
Rwork0.237 6609 -
obs--99.72 %

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