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- PDB-3ig9: Small outer capsid protein (SOC) of bacteriophage RB69 -

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Basic information

Entry
Database: PDB / ID: 3ig9
TitleSmall outer capsid protein (SOC) of bacteriophage RB69
ComponentsSoc small outer capsid protein
KeywordsVIRAL PROTEIN / Alpha/Beta structure
Function / homology
Function and homology information


viral capsid, decoration
Similarity search - Function
Small outer capsid protein Soc / Small outer capsid protein / Small outer capsid protein superfamily / Small outer capsid protein / Outer Surface Protein A; domain 3 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Small outer capsid protein
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsLi, Q. / Fokine, A. / O'Donnell, E. / Rao, V.B. / Rossmann, M.G.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure of the Small Outer Capsid Protein, Soc: A Clamp for Stabilizing Capsids of T4-like Phages
Authors: Qin, L. / Fokine, A. / O'Donnell, E. / Rao, V.B. / Rossmann, M.G.
History
DepositionJul 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soc small outer capsid protein
B: Soc small outer capsid protein
C: Soc small outer capsid protein
D: Soc small outer capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5308
Polymers34,2544
Non-polymers2764
Water5,567309
1
A: Soc small outer capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6332
Polymers8,5641
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Soc small outer capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6332
Polymers8,5641
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Soc small outer capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6332
Polymers8,5641
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Soc small outer capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6332
Polymers8,5641
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.128, 49.128, 198.674
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsAuthors state that the protein forms trimers in virus but is monomer in solution.

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Components

#1: Protein
Soc small outer capsid protein


Mass: 8563.533 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: soc / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Y5B1
#2: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.02 Å3/Da / Density % sol: 39.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG 8000; 0.1 M imidazole; 0.2 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.072 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.9→32 Å / Num. all: 21202 / Num. obs: 21202 / % possible obs: 99.2 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 33.2

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Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→32.312 Å / SU ML: 0.28 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 1135 5.35 %RANDOM
Rwork0.1811 ---
obs0.1837 21200 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.332 Å2 / ksol: 0.328 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→32.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 20 309 2677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042437
X-RAY DIFFRACTIONf_angle_d0.7643313
X-RAY DIFFRACTIONf_dihedral_angle_d15.091834
X-RAY DIFFRACTIONf_chiral_restr0.056357
X-RAY DIFFRACTIONf_plane_restr0.004431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.98650.27881640.20722455X-RAY DIFFRACTION99
1.9865-2.09120.27551280.18412509X-RAY DIFFRACTION100
2.0912-2.22220.23141220.17852537X-RAY DIFFRACTION99
2.2222-2.39370.2381440.18322473X-RAY DIFFRACTION99
2.3937-2.63450.25761680.18992503X-RAY DIFFRACTION100
2.6345-3.01540.26241400.19822519X-RAY DIFFRACTION100
3.0154-3.79820.22821380.16332537X-RAY DIFFRACTION100
3.7982-32.31670.1661310.1642532X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.4141-0.5662-0.62640.9094-0.46141.4036-0.09160.2432-0.02580.01770.0395-0.11340.03790.1477-0.02360.0591-0.04380.00920.1954-0.07190.0941-8.26721.4511110.1074
22.21740.0134-0.39321.25170.90160.5707-0.15390.11590.12890.22670.18710.27250.0249-0.3541-0.13210.1780.11080.04810.22130.08250.1473
32.7279-1.1131-0.5791.41280.42350.92310.0986-0.0382-0.20420.026-0.10860.2543-0.1155-0.07870.03390.08950.01620.01820.0954-0.00970.1251
41.0083-0.60991.0461.5675-0.44020.29060.11230.10970.1391-0.0181-0.1639-0.21-0.00120.15390.00850.1414-0.0050.03190.11840.01760.1095
Refinement TLS groupSelection details: chain D

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