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- PDB-3fzb: Crystal structure of the tail terminator protein from phage lambd... -

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Basic information

Entry
Database: PDB / ID: 3fzb
TitleCrystal structure of the tail terminator protein from phage lambda (gpU-WT)
ComponentsMinor tail protein U
KeywordsVIRAL PROTEIN / Mixed Alpha-Beta fold
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / host cell cytoplasm
Similarity search - Function
Phage minor tail protein U / Minor tail protein U-like / GpU-like superfamily / Phage minor tail protein U / Phage tail protein-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tail tube terminator protein
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPell, L.G. / Liu, A. / Edmonds, E. / Donaldson, L.W. / Howell, P.L. / Davidson, A.R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The X-ray crystal structure of the phage lambda tail terminator protein reveals the biologically relevant hexameric ring structure and demonstrates a conserved mechanism of tail termination ...Title: The X-ray crystal structure of the phage lambda tail terminator protein reveals the biologically relevant hexameric ring structure and demonstrates a conserved mechanism of tail termination among diverse long-tailed phages.
Authors: Pell, L.G. / Liu, A. / Edmonds, L. / Donaldson, L.W. / Howell, P.L. / Davidson, A.R.
History
DepositionJan 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / struct_biol / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Minor tail protein U
B: Minor tail protein U
C: Minor tail protein U
D: Minor tail protein U
E: Minor tail protein U
F: Minor tail protein U
G: Minor tail protein U
H: Minor tail protein U
I: Minor tail protein U
J: Minor tail protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,70213
Polymers149,41410
Non-polymers2883
Water1,964109
1
A: Minor tail protein U
B: Minor tail protein U
F: Minor tail protein U
H: Minor tail protein U
I: Minor tail protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8997
Polymers74,7075
Non-polymers1922
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-42 kcal/mol
Surface area27390 Å2
MethodPISA
2
C: Minor tail protein U
D: Minor tail protein U
E: Minor tail protein U
G: Minor tail protein U
J: Minor tail protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8036
Polymers74,7075
Non-polymers961
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-37 kcal/mol
Surface area27790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.100, 127.990, 82.910
Angle α, β, γ (deg.)90.00, 108.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Minor tail protein U


Mass: 14941.400 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Gene: U / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus / References: UniProt: P03732
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Tri-sodium citrate, 2.2M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 18, 2006
RadiationMonochromator: Osmic optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→70.1 Å / Num. all: 36045 / Num. obs: 36045 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.93 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 8.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.93 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→70.1 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.309 1788 5 %Random
Rwork0.236 ---
all0.236 36045 --
obs0.236 36045 --
Refinement stepCycle: LAST / Resolution: 2.8→70.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9625 0 15 109 9749
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5

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