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- PDB-3ige: Small outer capsid protein (Soc) from bacteriophage RB69 -

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Basic information

Entry
Database: PDB / ID: 3ige
TitleSmall outer capsid protein (Soc) from bacteriophage RB69
ComponentsSoc small outer capsid protein
KeywordsVIRAL PROTEIN / Alpha/Beta protein
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 / MOLECULAR REPLACEMENT / Resolution: 2.254 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2654
Polymers17,1272
Non-polymers1382
Water2,162120
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
Unit cell
Length a, b, c (Å)39.220, 88.613, 81.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
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.: 2
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.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.08 Å3/Da / Density % sol: 40.82 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.54→23.6 Å / Num. obs: 7033 / % possible obs: 99.6 % / Redundancy: 5.4 % / Rsym value: 0.058 / Net I/σ(I): 21.2

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structure of the Soc protein from bacteriophage RB69 (hexagonal crystal form).

Resolution: 2.254→23.595 Å / SU ML: 0.38 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 334 4.76 %random
Rwork0.2169 ---
obs0.2189 7023 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.408 Å2 / ksol: 0.316 e/Å3
Refinement stepCycle: LAST / Resolution: 2.254→23.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 10 120 1298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021212
X-RAY DIFFRACTIONf_angle_d0.4211648
X-RAY DIFFRACTIONf_dihedral_angle_d11.3414
X-RAY DIFFRACTIONf_chiral_restr0.03178
X-RAY DIFFRACTIONf_plane_restr0.003214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2545-2.83960.35131670.25593286X-RAY DIFFRACTION100
2.8396-23.59590.22351670.19763403X-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)
1refined2.23420.26250.81362.37181.16731.03550.23010.0658-0.1947-0.1277-0.1324-0.06030.4588-0.1272-0.0870.2889-0.0268-0.04460.1479-0.01190.1238-8.3440.811711.6614
22.63610.1321-1.71010.5894-0.24773.67510.50280.14810.3807-0.1109-0.18210.1512-0.4247-0.171-0.32280.1872-0.01610.04880.10950.05470.1249
Refinement TLS groupSelection details: chain B

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