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- PDB-2poh: Structure of Phage P22 Tail Needle gp26 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2poh
TitleStructure of Phage P22 Tail Needle gp26
ComponentsHead completion protein
KeywordsVIRAL PROTEIN / trimeric coiled-coil / triple beta-helix / heptad / membrane-penetration / fiber
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, short tail mechanism / virus tail / symbiont genome entry into host cell via pore formation in plasma membrane
Similarity search - Function
Helix Hairpins - #940 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Tail needle protein gp26 / Tail needle protein gp26
Similarity search - Component
Biological speciesSalmonella phage P22-pbi (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 2.1 Å
AuthorsOlia, A.S. / Cingolani, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structure of phage P22 cell envelope-penetrating needle.
Authors: Olia, A.S. / Casjens, S. / Cingolani, G.
History
DepositionApr 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 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: Head completion protein
B: Head completion protein
C: Head completion protein
D: Head completion protein
E: Head completion protein
F: Head completion protein


Theoretical massNumber of molelcules
Total (without water)149,1436
Polymers149,1436
Non-polymers00
Water15,961886
1
A: Head completion protein
B: Head completion protein
C: Head completion protein


Theoretical massNumber of molelcules
Total (without water)74,5723
Polymers74,5723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Head completion protein
E: Head completion protein
F: Head completion protein


Theoretical massNumber of molelcules
Total (without water)74,5723
Polymers74,5723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.398, 114.029, 171.917
Angle α, β, γ (deg.)90.00, 90.74, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAsymetric unit contains 2 trimers, the trimer being biologically active unit

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Components

#1: Protein
Head completion protein


Mass: 24857.213 Da / Num. of mol.: 6 / Mutation: L222M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage P22-pbi (virus) / Genus: P22-like viruses / Species: Enterobacteria phage P22 / Gene: 26 / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8LTG5, UniProt: P35837*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 886 / 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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 8% PEG8000; 0.1M Ammonium Sulfate, 0.05M NaCl, 0.1M Sodium Acetate pH4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONNSLS X6A10.9790.979
SYNCHROTRONCHESS F220.9760.976
SYNCHROTRONSSRL BL9-230.970.97
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMay 14, 2005
ADSC QUANTUM 2102CCDJul 25, 2006
3
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9761
30.971
ReflectionResolution: 2.1→40 Å / Num. all: 90017 / Num. obs: 90017 / % possible obs: 99.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.072 / Net I/σ(I): 15.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.353 / % possible all: 98.7

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Highest resolution: 2.1 Å / Num. parameters: 85 / Num. restraintsaints: 158758 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF). The data is twinned with twinning operators: h, -k, -l, and corresponding twin fractions 0.23239.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 --RANDOM
all0.1669 85617 --
obs--94.3 %-
Displacement parametersBiso mean: 28.3 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 11261 /
FreeObs
Luzzati sigma a0.8007 Å0.8835 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10375 0 0 886 11261
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0.283
X-RAY DIFFRACTIONs_from_restr_planes0.0343
X-RAY DIFFRACTIONs_zero_chiral_vol0.051
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.054
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.1
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.033
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.067
X-RAY DIFFRACTIONs_approx_iso_adps0.06
LS refinement shellResolution: 2.1→2.169 Å /
Rfactor% reflection
Rwork0.174 -
obs-98.46 %

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