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Basic information

Entry
Database: PDB / ID: 5nxf
TitleCrystal structure of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34, residues 795 to 1289, at 1.9 Angstrom.
ComponentsLong-tail fiber proximal subunit
KeywordsVIRAL PROTEIN / CAUDOVIRALES / MYOVIRIDAE
Function / homology: / Long-tail fiber proximal subunit, C-terminal, second / : / Long-tail fiber proximal subunit, C-terminal, trimerization domain / virus tail, fiber / ACETATE ION / PHOSPHATE ION / UREA / Long-tail fiber proximal subunit
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNamura, M. / van Raaij, M.J. / Kanamaru, S.
Funding support Spain, Japan, 6items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2008-01588 Spain
Spanish Ministry of Economy and CompetitivenessBFU2011-24843
Spanish Ministry of Economy and CompetitivenessBFU2014-53425-P
Spanish Ministry of Economy and CompetitivenessBFU2014-61367-EXP Spain
European CommissionNMP4-CT-2006-033256 Spain
Japan Society for the Promotion of ScienceJP25440066 Japan
Citation
Journal: Viruses / Year: 2017
Title: Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34.
Authors: Granell, M. / Namura, M. / Alvira, S. / Kanamaru, S. / van Raaij, M.J.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Crystallization of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34.
Authors: Granell, M. / Namura, M. / Alvira, S. / Garcia-Doval, C. / Singh, A.K. / Gutsche, I. / van Raaij, M.J. / Kanamaru, S.
History
DepositionMay 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_id_CSD / _citation.journal_id_ISSN ..._citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _entity.formula_weight / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Long-tail fiber proximal subunit
B: Long-tail fiber proximal subunit
C: Long-tail fiber proximal subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,51027
Polymers165,4593
Non-polymers2,05224
Water32,8051821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Analytical centrifugation shows the protein is a trimer., native gel electrophoresis, On SDS-PAGE without heating the sample, the protein runs as a trimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70720 Å2
ΔGint-398 kcal/mol
Surface area52700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.107, 75.943, 149.128
Angle α, β, γ (deg.)90.00, 90.21, 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 Long-tail fiber proximal subunit / Gene product 34 / gp34


Mass: 55152.875 Da / Num. of mol.: 3 / Fragment: UNP residues 781-1289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 34 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: P18771

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Non-polymers , 6 types, 1845 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1821 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.2 %
Description: Clustered bar-shaped and rhombus-shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: between 4 and 7 % (w/v) PEG 6000 100 mM TrisHCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.9→46.12 Å / Num. obs: 161501 / % possible obs: 99 % / Redundancy: 4.9 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 10
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 23029 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UXF

4uxf


Resolution: 1.9→46.12 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.935 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.114 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20785 1957 1.2 %RANDOM
Rwork0.17106 ---
obs0.17151 159525 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.891 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å21.59 Å2
2---0.47 Å20 Å2
3---1.05 Å2
Refinement stepCycle: 1 / Resolution: 1.9→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11299 0 130 1821 13250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211642
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210372
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.94615825
X-RAY DIFFRACTIONr_angle_other_deg0.943324094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28151480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31424.519520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.334151745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.481569
X-RAY DIFFRACTIONr_chiral_restr0.0850.21797
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022403
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4032.525932
X-RAY DIFFRACTIONr_mcbond_other1.4032.5195928
X-RAY DIFFRACTIONr_mcangle_it2.2053.7677406
X-RAY DIFFRACTIONr_mcangle_other2.2043.7687407
X-RAY DIFFRACTIONr_scbond_it1.512.6385710
X-RAY DIFFRACTIONr_scbond_other1.512.6385711
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3793.9128420
X-RAY DIFFRACTIONr_long_range_B_refined5.64231.31513429
X-RAY DIFFRACTIONr_long_range_B_other5.64231.31613430
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.896→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 159 -
Rwork0.244 11143 -
obs--93.92 %

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