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- PDB-2or1: RECOGNITION OF A DNA OPERATOR BY THE REPRESSOR OF PHAGE 434. A VI... -

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Basic information

Entry
Database: PDB / ID: 2or1
TitleRECOGNITION OF A DNA OPERATOR BY THE REPRESSOR OF PHAGE 434. A VIEW AT HIGH RESOLUTION
Components
  • 434 REPRESSOR
  • DNA (5'-D(*AP*AP*GP*TP*AP*CP*AP*AP*AP*CP*TP*TP*TP*CP*TP*TP*G P*TP*AP*T)-3')
  • DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*GP*AP*AP*AP*GP*TP*TP*TP*GP*T P*AP*CP*T)-3')
KeywordsGENE REGULATION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Repressor protein CI
Similarity search - Component
Biological speciesPhage 434 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsAggarwal, A.K. / Rodgers, D.W. / Drottar, M. / Ptashne, M. / Harrison, S.C.
Citation
Journal: Science / Year: 1988
Title: Recognition of a DNA operator by the repressor of phage 434: a view at high resolution.
Authors: Aggarwal, A.K. / Rodgers, D.W. / Drottar, M. / Ptashne, M. / Harrison, S.C.
#1: Journal: Nature / Year: 1987
Title: Structure of the Repressor-Operator Complex of Bacteriophage 434
Authors: Anderson, J.E. / Ptashne, M. / Harrison, S.C.
History
DepositionSep 5, 1989Deposition site: BNL / Processing site: NDB
Revision 1.0Sep 5, 1989Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*AP*GP*TP*AP*CP*AP*AP*AP*CP*TP*TP*TP*CP*TP*TP*G P*TP*AP*T)-3')
B: DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*GP*AP*AP*AP*GP*TP*TP*TP*GP*T P*AP*CP*T)-3')
L: 434 REPRESSOR
R: 434 REPRESSOR


Theoretical massNumber of molelcules
Total (without water)27,3844
Polymers27,3844
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.300, 65.000, 27.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*AP*AP*GP*TP*AP*CP*AP*AP*AP*CP*TP*TP*TP*CP*TP*TP*G P*TP*AP*T)-3')


Mass: 6106.990 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*GP*AP*AP*AP*GP*TP*TP*TP*GP*T P*AP*CP*T)-3')


Mass: 6156.027 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein 434 REPRESSOR


Mass: 7560.542 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Phage 434 (virus) / Genus: Lambda-like viruses / Species: Enterobacteria phage lambda / References: UniProt: P16117
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 300011
3NACL11
4MGCL211
5SPERMINE11
6WATER12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formula
11 mMDNA1
22 mMprotein1
3100 mM1NaCl
4120 mM1MgCl2
512-14 %PEG30001
61

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Num. all: 9914 / Num. obs: 6019 / % possible obs: 60.7 % / Rmerge(I) obs: 0.123

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.179 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 814 0 44 1826
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS

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