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- PDB-4zku: P22 Tail Needle Gp26 crystallized at pH 10.0 -

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Basic information

Entry
Database: PDB / ID: 4zku
TitleP22 Tail Needle Gp26 crystallized at pH 10.0
ComponentsTail needle protein gp26
KeywordsVIRAL PROTEIN / P22 / Tail Needle / Membrane penetration
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
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSankhala, R.S. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 100888 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions.
Authors: Bhardwaj, A. / Sankhala, R.S. / Olia, A.S. / Brooke, D. / Casjens, S.R. / Taylor, D.J. / Prevelige, P.E. / Cingolani, G.
History
DepositionApr 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Data collection / Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Jan 13, 2016Group: Database references
Revision 1.4Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail needle protein gp26
B: Tail needle protein gp26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3036
Polymers50,1512
Non-polymers1514
Water8,395466
1
A: Tail needle protein gp26
hetero molecules

A: Tail needle protein gp26
hetero molecules

A: Tail needle protein gp26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4549
Polymers75,2273
Non-polymers2276
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area23440 Å2
ΔGint-139 kcal/mol
Surface area24210 Å2
MethodPISA
2
B: Tail needle protein gp26
hetero molecules

B: Tail needle protein gp26
hetero molecules

B: Tail needle protein gp26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4549
Polymers75,2273
Non-polymers2276
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area23450 Å2
ΔGint-143 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.200, 43.200, 271.234
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-301-

CL

21A-302-

CA

31B-301-

CL

41B-302-

CA

51A-472-

HOH

61A-497-

HOH

71A-498-

HOH

81A-501-

HOH

91A-512-

HOH

101B-453-

HOH

111B-523-

HOH

121B-535-

HOH

131B-538-

HOH

141B-624-

HOH

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Components

#1: Protein Tail needle protein gp26 / Head completion protein / Packaged DNA stabilization protein / Tail accessory factor gp26


Mass: 25075.744 Da / Num. of mol.: 2 / Mutation: L222M
Source method: isolated from a genetically manipulated source
Details: Bacteriophage P22 / Source: (gene. exp.) Enterobacteria phage P22 (virus) / Gene: 26 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35837
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10 / Details: 40% PEG 4000, 0.1M CAPS pH 10.0 / PH range: 10

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 9, 2008
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 19166 / % possible obs: 96.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.083 / Net I/σ(I): 13.66
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4.4 / % possible all: 84.6

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Processing

Software
NameVersionClassification
PHENIXDEV_2016refinement
HKL-2000data reduction
HKL-2000data scaling
AUTOMARdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2POH

2poh


Resolution: 2.5→28.82 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.18 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.225 979 5.12 %Thin resolution shell
Rwork0.184 ---
obs0.191 19111 96.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 4 466 3154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032706
X-RAY DIFFRACTIONf_angle_d0.6553676
X-RAY DIFFRACTIONf_dihedral_angle_d12.818972
X-RAY DIFFRACTIONf_chiral_restr0.034454
X-RAY DIFFRACTIONf_plane_restr0.002482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5177-2.64770.33331470.21682373X-RAY DIFFRACTION89
2.6477-2.80930.26491520.20582448X-RAY DIFFRACTION92
2.8093-3.01950.2148980.18552567X-RAY DIFFRACTION95
3.0195-3.31120.2141460.20632540X-RAY DIFFRACTION93
3.3112-3.76290.20941530.17442468X-RAY DIFFRACTION93
3.7629-4.64310.21971310.15642514X-RAY DIFFRACTION93
4.6431-9.37770.19661300.19892515X-RAY DIFFRACTION92

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