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- PDB-5nxh: Crystal structure of the carboxy-terminal region of the bacteriop... -

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Basic information

Entry
Database: PDB / ID: 5nxh
TitleCrystal structure of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34, residues 744-1289 at 2.9 Angstrom resolution
ComponentsLong-tail fiber proximal subunit
KeywordsVIRAL PROTEIN / CAUDOVIRALES / MYOVIRIDAE / STRUCTURAL PROTEIN
Function / homology: / Long-tail fiber proximal subunit, C-terminal, second / : / Long-tail fiber proximal subunit, C-terminal, trimerization domain / virus tail, fiber / Long-tail fiber proximal subunit
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsNamura, M. / van Raaij, M.J. / Kanamaru, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
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 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)182,5374
Polymers182,4453
Non-polymers921
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Protein sediments as a trimer, native gel electrophoresis, Protein runs as a trimer on SDS-PAGE if sample is not heated before loading.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70630 Å2
ΔGint-406 kcal/mol
Surface area60910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.297, 76.133, 139.868
Angle α, β, γ (deg.)90.00, 97.62, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 744 - 1289 / Label seq-ID: 19 - 564

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Long-tail fiber proximal subunit / Gene product 34 / gp34


Mass: 60815.098 Da / Num. of mol.: 3 / Fragment: UNP residue 726-1289
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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 3.11 Å3/Da / Density % sol: 60.43 % / Description: Semi-ellipsoidal-shaped plates
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 4-7% (w/v) PEG 6000 100 mM Tris-HCl pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.89→45.18 Å / Num. obs: 48930 / % possible obs: 96.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 69.5 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.4
Reflection shellResolution: 2.89→3.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3 / Num. unique obs: 6784 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NXF

5nxf


Resolution: 2.89→45.18 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.894 / SU B: 20.699 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26262 1911 3.9 %RANDOM
Rwork0.19962 ---
obs0.2021 47006 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 64.78 Å2
Baniso -1Baniso -2Baniso -3
1--2.68 Å20 Å2-7.86 Å2
2--3.05 Å20 Å2
3---1.67 Å2
Refinement stepCycle: 1 / Resolution: 2.89→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12441 0 6 350 12797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212686
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211394
X-RAY DIFFRACTIONr_angle_refined_deg1.481.93917273
X-RAY DIFFRACTIONr_angle_other_deg0.979326477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14451635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22224.734564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.297152007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5171575
X-RAY DIFFRACTIONr_chiral_restr0.0850.21984
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022571
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_it4.56.6246549
X-RAY DIFFRACTIONr_mcbond_other4.56.6236548
X-RAY DIFFRACTIONr_mcangle_it7.2059.9298181
X-RAY DIFFRACTIONr_mcangle_other7.2059.938182
X-RAY DIFFRACTIONr_scbond_it3.8916.7196137
X-RAY DIFFRACTIONr_scbond_other3.896.7196137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5139.9959093
X-RAY DIFFRACTIONr_long_range_B_refined10.1276.38813475
X-RAY DIFFRACTIONr_long_range_B_other10.11676.41913464
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A29080
12B29080
21A29118
22C29118
31B29126
32C29126
LS refinement shellResolution: 2.887→2.962 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 130 -
Rwork0.352 3004 -
obs--83.91 %

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