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Basic information

Entry
Database: PDB / ID: 4uxe
TitleCrystal structure of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34, P21 selenomethionine crystal
ComponentsLARGE TAIL FIBER PROTEIN P34
KeywordsVIRAL PROTEIN / CAUDOVIRALES / MYOVIRIDAE / TRIPLE BETA-HELIX
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 / SAD / Resolution: 2 Å
AuthorsGranell, M. / Alvira, S. / Garcia-Doval, C. / Singh, A.K. / van Raaij, M.J.
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.,Sect.F / 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
DepositionAug 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_first ..._citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_sheet / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LARGE TAIL FIBER PROTEIN P34
B: LARGE TAIL FIBER PROTEIN P34
C: LARGE TAIL FIBER PROTEIN P34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,16910
Polymers134,5243
Non-polymers6457
Water29,1661619
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53280 Å2
ΔGint-281 kcal/mol
Surface area43050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.840, 76.330, 116.960
Angle α, β, γ (deg.)90.00, 99.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LARGE TAIL FIBER PROTEIN P34 / PROXIMAL LONG TAIL FIBRE PROTEIN GP34 / PROTEIN GP34


Mass: 44841.340 Da / Num. of mol.: 3 / Fragment: CARBOXY-TERMINAL REGION, RESIDUES 894-1289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE T4 (virus)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSMZ), DSM 4505
Production host: ESCHERICHIA COLI B (bacteria) / Variant (production host): BL834(DE3) / References: UniProt: P18771
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1619 / Source method: isolated from a natural source / Formula: H2O
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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 8.5
Details: 10-16% (W/V) PEG 6000, 12-22% (V/V) GLYCEROL, 0.1 M TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2012 / Details: HORIZONTAL AND VERTICAL FOCUSSING MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 109012 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.6 / % possible all: 99.9

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Processing

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

Resolution: 2→29.62 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.593 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17533 2205 2 %THIN SHELLS
Rwork0.13971 ---
obs0.14045 106789 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: 19.997 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å21.57 Å2
2--0.11 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9091 0 42 1619 10752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229388
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.93212768
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78651198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00724.217434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.102151459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6151564
X-RAY DIFFRACTIONr_chiral_restr0.10.21425
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217245
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.24308
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.26349
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.21310
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.259
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.94825902
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7339568
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.75663486
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.989103195
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→2.121 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.207 346 -
Rwork0.162 17167 -
obs--100 %

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