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- PDB-3lj5: Full Length Bacteriophage P22 Portal Protein -

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Basic information

Entry
Database: PDB / ID: 3lj5
TitleFull Length Bacteriophage P22 Portal Protein
ComponentsPortal protein
KeywordsVIRAL PROTEIN / portal protein / DNA ejection / molecular motor / DNA packaging / Podoviridae / virus assembly / tail tube / trunk domain / Late protein
Function / homologyPhage P22-like portal protein / Phage P22-like portal protein / viral DNA genome packaging, headful / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / virion assembly / Portal protein
Function and homology information
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.497 Å
AuthorsOlia, A.S. / Cingolani, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Three-dimensional structure of a viral genome-delivery portal vertex.
Authors: Olia, A.S. / Prevelige, P.E. / Johnson, J.E. / Cingolani, G.
History
DepositionJan 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein


Theoretical massNumber of molelcules
Total (without water)993,95312
Polymers993,95312
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130630 Å2
ΔGint-560 kcal/mol
Surface area360060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)408.949, 408.949, 260.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A
211chain B
311chain C
411chain D
511chain E
611chain F
711chain G
811chain H
911chain I
1011chain J
1111chain K
1211chain L

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Components

#1: Protein
Portal protein / Protein gp1


Mass: 82829.375 Da / Num. of mol.: 12 / Fragment: UNP residues 1-725
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Gene: 1, gp1 / Plasmid: pET-22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P26744

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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: 5.47 Å3/Da / Density % sol: 77.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 30% tert-Butanol, 70mM sodium chloride, 2.5% PEG 400, 0.1M sodium acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2001 / Details: bent conical Si-mirror (Rh coating)
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 7.497→60 Å / Num. all: 27324 / Num. obs: 27188 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 236.6 Å2 / Rsym value: 0.095 / Net I/σ(I): 12.7
Reflection shellResolution: 7.5→7.67 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.777 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 7.497→59.484 Å / SU ML: 1.1 / σ(F): 0.05 / Phase error: 25.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 1877 7.34 %
Rwork0.1874 --
obs0.193 25572 92.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 187.987 Å2 / ksol: 0.255 e/Å3
Refinement stepCycle: LAST / Resolution: 7.497→59.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms61512 0 0 0 61512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01462664
X-RAY DIFFRACTIONf_angle_d1.16885368
X-RAY DIFFRACTIONf_dihedral_angle_d18.55721660
X-RAY DIFFRACTIONf_chiral_restr0.0739552
X-RAY DIFFRACTIONf_plane_restr0.00511472
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5126X-RAY DIFFRACTIONPOSITIONAL
12B5126X-RAY DIFFRACTIONPOSITIONAL0
13C5126X-RAY DIFFRACTIONPOSITIONAL0.001
14D5126X-RAY DIFFRACTIONPOSITIONAL0
15E5126X-RAY DIFFRACTIONPOSITIONAL0.001
16F5126X-RAY DIFFRACTIONPOSITIONAL0
17G5126X-RAY DIFFRACTIONPOSITIONAL0
18H5126X-RAY DIFFRACTIONPOSITIONAL0
19I5126X-RAY DIFFRACTIONPOSITIONAL0.001
110J5126X-RAY DIFFRACTIONPOSITIONAL0
111K5126X-RAY DIFFRACTIONPOSITIONAL0.001
112L5126X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.497-7.69910.39451280.28081494X-RAY DIFFRACTION76
7.6991-7.92510.32921350.23141690X-RAY DIFFRACTION87
7.9251-8.18030.31941360.20651728X-RAY DIFFRACTION89
8.1803-8.47190.2851350.1791775X-RAY DIFFRACTION91
8.4719-8.810.2771430.15531836X-RAY DIFFRACTION93
8.81-9.20960.20991410.12441827X-RAY DIFFRACTION95
9.2096-9.69320.21611510.1141901X-RAY DIFFRACTION96
9.6932-10.29760.18971500.10471878X-RAY DIFFRACTION96
10.2976-11.0880.19861490.10361868X-RAY DIFFRACTION96
11.088-12.19510.1771530.10441915X-RAY DIFFRACTION97
12.1951-13.93990.2321520.13121896X-RAY DIFFRACTION97
13.9399-17.48850.29391550.23261929X-RAY DIFFRACTION97
17.4885-59.48630.34551490.36221958X-RAY DIFFRACTION97
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)
10.0401-0.15720.02780.0696-0.2185-0.1927-0.3018-0.04140.60060.1447-0.3117-0.4946-1.0196-0.08720.65130.55180.177-0.31730.14330.06530.7046123.516252.978358.0463
2-0.18680.05360.30980.09910.14950.2652-0.1638-0.0130.64710.1344-0.1927-0.1907-0.40430.01470.09940.4013-0.0163-0.35220.48960.05290.5322145.41750.819751.5737
30.27220.050.02780.4568-0.2879-0.1263-0.25760.04260.4197-0.0328-0.287-0.0582-0.3180.2645-0.46690.28830.0291-0.34580.49580.17060.7357160.925545.951835.3452
40.20390.0360.1090.3756-0.0736-0.07770.11830.06420.6363-0.14250.0214-0.0953-0.2480.10620.32550.15220.1778-0.03440.23330.07970.6263165.891138.961513.9533
50.03630.07790.01020.2024-0.576-0.51060.3463-0.17420.1886-0.28040.0545-0.1352-0.67940.14050.32570.0997-0.01810.17220.25470.01970.5736158.920132.6384-6.6357
6-0.1044-0.0984-0.23380.3313-0.5137-0.0845-0.10220.20430.2225-0.2549-0.0192-0.0925-0.84230.25490.22710.4327-0.18030.21020.28690.0230.324141.910727.7935-21.1957
7-0.15060.2405-0.01720.4926-0.49990.08810.28140.19370.3677-0.18680.2530.2741-0.5939-0.11990.83130.264-0.04190.02190.16940.14710.1839119.643225.8902-25.7456
80.0363-0.03470.05230.4221-0.1340.0295-0.0231-0.01880.0422-0.06280.03040.1089-0.18290.05170.27670.2925-0.2202-0.0170.23720.11120.335897.758727.6597-19.2062
90.1619-0.05020.20010.7939-0.67870.4715-0.04510.10270.15910.06150.27390.2156-0.5038-0.17530.80070.3204-0.1851-0.00620.36160.13940.130382.321432.7154-3.04
100.09360.03430.03740.2376-0.48980.00670.10730.19540.25490.00980.0910.1086-0.3744-0.15980.56540.12040.00880.10440.26580.11550.256977.361839.580618.1579
11-0.1109-0.09430.07330.491-0.06970.05030.14880.11380.5833-0.07790.1746-0.086-0.2167-0.18950.78170.37980.18390.01630.40870.19610.37184.188846.140438.8714
12-0.0216-0.11890.06710.18780.00290.1972-0.05590.03230.0469-0.0823-0.0748-0.0518-0.2880.03430.28520.4349-0.0232-0.13830.201-0.03040.3561101.447751.098253.4586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L

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