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- PDB-3fz2: Crystal structure of the tail terminator protein from phage lambd... -

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Basic information

Entry
Database: PDB / ID: 3fz2
TitleCrystal structure of the tail terminator protein from phage lambda (gpU-D74A)
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 / SYNCHROTRON / SAD / Resolution: 2.7 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 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
K: Minor tail protein U
L: Minor tail protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,83125
Polymers181,58212
Non-polymers1,24913
Water4,432246
1
A: Minor tail protein U
B: Minor tail protein U
E: Minor tail protein U
F: Minor tail protein U
I: Minor tail protein U
K: Minor tail protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,46413
Polymers90,7916
Non-polymers6727
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-40.1 kcal/mol
Surface area34380 Å2
MethodPISA
2
C: Minor tail protein U
D: Minor tail protein U
G: Minor tail protein U
H: Minor tail protein U
J: Minor tail protein U
L: Minor tail protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,36812
Polymers90,7916
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-41 kcal/mol
Surface area35180 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17720 Å2
ΔGint-107.5 kcal/mol
Surface area65840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.370, 125.400, 211.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Minor tail protein U


Mass: 15131.867 Da / Num. of mol.: 12 / Mutation: D74A
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.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 3.19 Å3/Da / Density % sol: 61.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Di-ammonium tartrate, 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: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 18, 2006 / Details: Detector built at Brandeis University
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→46.84 Å / Num. all: 123255 / Num. obs: 123255 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.57 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.57 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→46.84 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 6103 4.9 %Random
Rwork0.233 ---
all0.233 123255 --
obs0.233 123255 --
Refinement stepCycle: LAST / Resolution: 2.7→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11947 0 65 246 12258
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.45
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.781

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