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- PDB-1zs4: Structure of bacteriophage lambda cII protein in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 1zs4
TitleStructure of bacteriophage lambda cII protein in complex with DNA
Components
  • (DNA - 27mer) x 2
  • Regulatory protein CII
Keywordstranscription/DNA / HELIX-TURN-HELIX / TRANSCRIPTION ACTIVATOR / transcription-DNA COMPLEX
Function / homology
Function and homology information


viral latency / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription activator CII / Bacteriophage CII protein / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional activator II
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJain, D. / Kim, Y. / Maxwell, K.L. / Beasley, S. / Gussin, G.N. / Edwards, A.M. / Darst, S.A.
CitationJournal: Mol.Cell / Year: 2005
Title: Crystal Structure of Bacteriophage lambdacII and Its DNA Complex.
Authors: Jain, D. / Kim, Y. / Maxwell, K.L. / Beasley, S. / Zhang, R. / Gussin, G.N. / Edwards, A.M. / Darst, S.A.
History
DepositionMay 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Advisory
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
U: DNA - 27mer
T: DNA - 27mer
A: Regulatory protein CII
B: Regulatory protein CII
C: Regulatory protein CII
D: Regulatory protein CII


Theoretical massNumber of molelcules
Total (without water)53,8706
Polymers53,8706
Non-polymers00
Water7,512417
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.771, 97.132, 59.869
Angle α, β, γ (deg.)90.00, 105.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA - 27mer


Mass: 8264.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC
#2: DNA chain DNA - 27mer


Mass: 8318.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC
#3: Protein
Regulatory protein CII


Mass: 9321.896 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Gene: CII / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03042
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.8
Details: PEG 550 MME, SODIUM ACETATE, pH 4.8, VAPOR DIFFUSION, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 55011
2Sodium acetate11
3PEG 55012

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.98396, 0.97903, 0.97922, 0.96384
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 24, 2004
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.983961
20.979031
30.979221
40.963841
ReflectionResolution: 1.7→50 Å / Num. obs: 54170 / % possible obs: 97.3 % / Rsym value: 0.067 / Net I/σ(I): 8.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→50 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.228 2608 RANDOM
Rwork0.209 --
all-59978 -
obs-54170 -
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 1100 0 417 3999

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