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- PDB-4zkp: P22 Tail Needle Gp26 crystallized at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 4zkp
TitleP22 Tail Needle Gp26 crystallized at pH 7.0
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: 2.1 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)GM100888 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 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Data collection / Database references
Revision 1.3Dec 2, 2015Group: Database references
Revision 1.4Jan 13, 2016Group: Database references
Revision 1.5Sep 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 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Sep 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
Water13,763764
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_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area23490 Å2
ΔGint-138 kcal/mol
Surface area24070 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_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area23560 Å2
ΔGint-134 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.846, 43.846, 272.319
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-300-

CA

21A-301-

CL

31B-300-

CA

41B-301-

CL

51A-473-

HOH

61A-495-

HOH

71A-504-

HOH

81A-572-

HOH

91A-715-

HOH

101A-773-

HOH

111B-474-

HOH

121B-479-

HOH

131B-500-

HOH

141B-577-

HOH

151B-582-

HOH

161B-703-

HOH

171B-705-

HOH

181B-737-

HOH

191B-766-

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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 764 / 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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 40% PEG 1000, 0.1M MOPS pH7.0 / PH range: pH7.0

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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: 2.1→30 Å / Num. obs: 32511 / % possible obs: 95.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.066 / Net I/σ(I): 16.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.55 / % possible all: 70.4

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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: 2.1→29.12 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 19.51 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1697 5.22 %Thin resolution shell
Rwork0.154 ---
obs0.158 32511 95.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 4 764 3452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022706
X-RAY DIFFRACTIONf_angle_d0.5773676
X-RAY DIFFRACTIONf_dihedral_angle_d13.852972
X-RAY DIFFRACTIONf_chiral_restr0.03454
X-RAY DIFFRACTIONf_plane_restr0.003482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1228-2.18410.2181500.19371840X-RAY DIFFRACTION66
2.1841-2.25310.2143790.1922278X-RAY DIFFRACTION86
2.2531-2.33180.24941770.17672519X-RAY DIFFRACTION91
2.3318-2.42280.22821680.17292535X-RAY DIFFRACTION93
2.4228-2.52990.2153920.17352575X-RAY DIFFRACTION96
2.5299-2.65890.23891740.1692479X-RAY DIFFRACTION93
2.6589-2.81890.1587830.1552657X-RAY DIFFRACTION96
2.8189-3.02610.15481720.14452516X-RAY DIFFRACTION93
3.0261-3.31180.2468770.15262638X-RAY DIFFRACTION96
3.3118-3.74940.16671670.13542526X-RAY DIFFRACTION93
3.7494-4.5790.14731670.12472503X-RAY DIFFRACTION93
4.579-8.13270.19671490.16382560X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0163-0.0077-0.00280.0211-0.00710.0048-0.0118-0.02980.01230.04860.02540.00790.00660.0157-0.0020.06770.0008-0.00160.0702-0.0129-0.0087-0.115625.9955-41.2664
20.0142-0.0006-0.00090.00920.00190.0010.00020.0054-0.0069-0.0110.0081-0.00690.0042-0.009800.057-0.007900.06120.01590.04821.516123.237157.9803
3-0.0007-0.00170.00340.00970.00170.00820.0069-0.0279-0.02240.04480.0128-0.01970.00860.0005-0.00640.09720.00490.00330.09030.0251-0.000922.026611.914995.2607
40.01140.00220.00170.009-0.00290.00320.0062-0.00030.0084-0.00440.01320.00940.00060.01220.00780.04390.00280.00470.0446-0.01650.039220.537214.8233194.174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 55 THROUGH 139 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 140 THROUGH 233 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 56 THROUGH 139 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 140 THROUGH 232 )

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