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- PDB-4uxg: Crystal structure of the carboxy-terminal region of the bacteriop... -

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Basic information

Entry
Database: PDB / ID: 4uxg
TitleCrystal structure of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34, R32 native 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 / MOLECULAR REPLACEMENT / Resolution: 3 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 1.0Sep 30, 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 1.3Jan 10, 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 / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet
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_sheet.number_strands
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

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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
D: LARGE TAIL FIBER PROTEIN P34
E: LARGE TAIL FIBER PROTEIN P34
F: LARGE TAIL FIBER PROTEIN P34
G: LARGE TAIL FIBER PROTEIN P34
H: LARGE TAIL FIBER PROTEIN P34
I: LARGE TAIL FIBER PROTEIN P34
J: LARGE TAIL FIBER PROTEIN P34
K: LARGE TAIL FIBER PROTEIN P34
L: LARGE TAIL FIBER PROTEIN P34


Theoretical massNumber of molelcules
Total (without water)534,72012
Polymers534,72012
Non-polymers00
Water00
1
A: LARGE TAIL FIBER PROTEIN P34
B: LARGE TAIL FIBER PROTEIN P34
C: LARGE TAIL FIBER PROTEIN P34


Theoretical massNumber of molelcules
Total (without water)133,6803
Polymers133,6803
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50880 Å2
ΔGint-272.1 kcal/mol
Surface area44300 Å2
MethodPISA
2
D: LARGE TAIL FIBER PROTEIN P34
E: LARGE TAIL FIBER PROTEIN P34
F: LARGE TAIL FIBER PROTEIN P34


Theoretical massNumber of molelcules
Total (without water)133,6803
Polymers133,6803
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50980 Å2
ΔGint-275.4 kcal/mol
Surface area44660 Å2
MethodPISA
3
G: LARGE TAIL FIBER PROTEIN P34
H: LARGE TAIL FIBER PROTEIN P34
I: LARGE TAIL FIBER PROTEIN P34


Theoretical massNumber of molelcules
Total (without water)133,6803
Polymers133,6803
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50990 Å2
ΔGint-276 kcal/mol
Surface area44740 Å2
MethodPISA
4
J: LARGE TAIL FIBER PROTEIN P34
K: LARGE TAIL FIBER PROTEIN P34
L: LARGE TAIL FIBER PROTEIN P34


Theoretical massNumber of molelcules
Total (without water)133,6803
Polymers133,6803
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50600 Å2
ΔGint-269.6 kcal/mol
Surface area44560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.489, 228.489, 1069.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 44559.973 Da / Num. of mol.: 12 / 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 BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: P18771

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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: 5 Å3/Da / Density % sol: 76 % / Description: NONE
Crystal growpH: 8.5
Details: 1.0-1.2 M AMMONIUM SULFATE, 6-16% (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: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2012 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 214066 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 55.6 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UXF

4uxf


Resolution: 3→29.986 Å / SU ML: 0.38 / σ(F): 1.36 / Phase error: 27.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 2999 1.4 %
Rwork0.2257 --
obs0.2261 213700 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.4 Å2
Refinement stepCycle: LAST / Resolution: 3→29.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36241 0 0 0 36241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00537024
X-RAY DIFFRACTIONf_angle_d0.89950370
X-RAY DIFFRACTIONf_dihedral_angle_d11.7813187
X-RAY DIFFRACTIONf_chiral_restr0.0395611
X-RAY DIFFRACTIONf_plane_restr0.0056676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.23140.32095450.28141856X-RAY DIFFRACTION100
3.2314-3.55610.29154440.247142129X-RAY DIFFRACTION100
3.5561-4.06960.24317560.22241850X-RAY DIFFRACTION100
4.0696-5.12310.2125310.193442046X-RAY DIFFRACTION99
5.1231-29.98710.24087230.223342820X-RAY DIFFRACTION100

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