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- PDB-1xwr: Crystal structure of the coliphage lambda transcription activator... -

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Basic information

Entry
Database: PDB / ID: 1xwr
TitleCrystal structure of the coliphage lambda transcription activator protein CII
ComponentsRegulatory protein CII
KeywordsDNA BINDING PROTEIN / all-alpha fold
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
ISOPROPYL ALCOHOL / Transcriptional activator II
Similarity search - Component
Biological speciesBacteriophage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.56 Å
AuthorsDatta, A.B. / Panjikar, S. / Weiss, M.S. / Chakrabarti, P. / Parrack, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of {lambda} CII: Implications for recognition of direct-repeat DNA by an unusual tetrameric organization
Authors: Datta, A.B. / Panjikar, S. / Weiss, M.S. / Chakrabarti, P. / Parrack, P.
History
DepositionNov 2, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: Regulatory protein CII
B: Regulatory protein CII
C: Regulatory protein CII
D: Regulatory protein CII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4727
Polymers44,2924
Non-polymers1803
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-74 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.907, 106.794, 119.784
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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.) Bacteriophage lambda (virus) / Gene: CII / Plasmid: pAB305 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03042
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.93 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: PEG 3350, isopropanol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG BW7A10.9836, 0.9841, 0.9949, 0.9733
SYNCHROTRONEMBL/DESY, HAMBURG X1320.8
SYNCHROTRONSPring-8 BL40B230.9796
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1YALE MIRRORSMADMx-ray1
2YALE MIRRORSSINGLE WAVELENGTHMx-ray1
3YALE MIRRORSSADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.98361
20.98411
30.99491
40.97331
50.81
60.97961
ReflectionResolution: 2.55→20 Å / Num. all: 13683 / Num. obs: 13650 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 77.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 22.4
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.56→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 950 7 %RANDOM
Rwork0.25 ---
all0.315 13649 --
obs0.25 13536 99.7 %-
Displacement parametersBiso mean: 46.04 Å2
Baniso -1Baniso -2Baniso -3
1--7.618 Å20 Å20 Å2
2--1.483 Å20 Å2
3---6.135 Å2
Refine analyzeLuzzati coordinate error obs: 0.467 Å
Refinement stepCycle: LAST / Resolution: 2.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 0 55 2485
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3

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