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- PDB-3o27: The crystal structure of C68 from the hybrid virus-plasmid pSSVx -

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Basic information

Entry
Database: PDB / ID: 3o27
TitleThe crystal structure of C68 from the hybrid virus-plasmid pSSVx
ComponentsPutative uncharacterized protein
KeywordsDNA BINDING PROTEIN / swapped-hairpin fold / transcription factor
Function / homologyPemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #10 / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain / Ribbon / DNA binding / Mainly Beta / SpoVT-AbrB domain-containing protein
Function and homology information
Biological speciesSulfolobus islandicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsD'Ambrosio, K. / De Simone, G.
CitationJournal: Biochem.J. / Year: 2011
Title: C68 from the Sulfolobus islandicus plasmid-virus pSSVx is a novel member of the AbrB-like transcription factor family.
Authors: Contursi, P. / D'Ambrosio, K. / Pirone, L. / Pedone, E. / Aucelli, T. / She, Q. / De Simone, G. / Bartolucci, S.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)15,5142
Polymers15,5142
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-32 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.720, 107.720, 107.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Putative uncharacterized protein


Mass: 7757.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus (archaea) / Strain: REY15/4 / Gene: orfc68 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus / References: UniProt: Q9P9J8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.36 Å3/Da / Density % sol: 63.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: 1.6 M sodium formate, 0.1 M Sodium acetate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 29, 2008
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 5275 / Num. obs: 5275 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 0.393
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 5.3 / Num. unique all: 528 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.289 384 RANDOM
Rwork0.252 --
all-5275 -
obs-5148 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 0 0 38 993
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_bond_d0.009
LS refinement shellResolution: 2.8→2.93 Å /
RfactorNum. reflection
Rfree0.402 48
Rwork0.335 -
obs-548

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