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- PDB-1zpq: STRUCTURE OF BACTERIOPHAGE LAMBDA CII protein -

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Basic information

Entry
Database: PDB / ID: 1zpq
TitleSTRUCTURE OF BACTERIOPHAGE LAMBDA CII protein
ComponentsRegulatory protein CII
Keywordstranscription activator / HELIX-TURN-HELIX / TRANSCRIPTION ACTIVATION / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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
Transcriptional activator II
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsJain, D. / Kim, Y. / Maxwell, K.L. / Beasley, S. / Gussin, G.N. / Edwards, A.M. / Joachimiak, A. / Darst, S.A. / Midwest Center for Structural Genomics (MCSG)
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 17, 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 1.3Oct 5, 2011Group: Structure summary
Revision 1.4Feb 14, 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: Regulatory protein CII
B: Regulatory protein CII
C: Regulatory protein CII
D: Regulatory protein CII


Theoretical massNumber of molelcules
Total (without water)44,2924
Polymers44,2924
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-80 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.560, 108.160, 111.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Regulatory protein CII


Mass: 11072.907 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03042
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.28 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979262 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979262 Å / Relative weight: 1
ReflectionResolution: 2.8→38.8 Å / Num. obs: 11571 / Redundancy: 6 % / Rsym value: 0.048 / Net I/σ(I): 8.9
Reflection shellResolution: 2.8→2.93 Å / Mean I/σ(I) obs: 2.61 / Rsym value: 0.398 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.8→38.8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.286 442 5 %RANDOM
Rwork0.255 ---
all0.257 ---
obs0.257 11571 96.5 %-
Refinement stepCycle: LAST / Resolution: 2.8→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 0 88 2480

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