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- PDB-1per: THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND O... -

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Basic information

Entry
Database: PDB / ID: 1per
TitleTHE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES
Components
  • DNA (5'-D(*AP*AP*GP*TP*AP*CP*AP*GP*TP*TP*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*AP*AP*CP*TP*GP*T P*AP*CP*T)-3')
  • PROTEIN (434 REPRESSOR)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-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
AuthorsRodgers, D.W. / Harrison, S.C.
Citation
Journal: Structure / Year: 1993
Title: The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites.
Authors: Rodgers, D.W. / Harrison, S.C.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: The Phage 434 OR2/R1-69 Complex at 2.5 Angstroms Resolution
Authors: Shimon, L.W. / Harrison, S.C.
#2: 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.
History
DepositionNov 9, 1993Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,3844
Polymers27,3844
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.900, 64.500, 27.800
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*GP*TP*TP*TP*TP*TP*CP*TP*TP*G P*TP*AP*T)-3')


Mass: 6128.986 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*AP*AP*CP*TP*GP*T P*AP*CP*T)-3')


Mass: 6134.031 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein 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.: 40 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.55 mMDNA1drop
215-17 %(w/v)PEG30001reservoir
380 mM1reservoirNaCl
4100 mM1reservoirMgCl2
52 mMspermine1reservoir
6100 mMMES1reservoirpH5.5

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 8311 / % possible obs: 83.8 % / Num. measured all: 20076 / Rmerge(I) obs: 0.083

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Processing

Software
NameClassification
CORELSrefinement
TNTrefinement
RefinementRfactor obs: 0.187 / Highest resolution: 2.5 Å / σ(I): 1.5
Details: THE FOLLOWING CLOSE CRYSTAL PACKING CONTACTS BETWEEN DNA CHAINS RELATED BY A TRANSLATION ALONG THE B AXIS ARE OBSERVED: C2 A 1 A - N3 T 1 B DIST= 1.68 N1 A 1 A - O4 T 1 B DIST= 1.72 N1 A 1 A ...Details: THE FOLLOWING CLOSE CRYSTAL PACKING CONTACTS BETWEEN DNA CHAINS RELATED BY A TRANSLATION ALONG THE B AXIS ARE OBSERVED: C2 A 1 A - N3 T 1 B DIST= 1.68 N1 A 1 A - O4 T 1 B DIST= 1.72 N1 A 1 A - N3 T 1 B DIST= 1.77 N1 A 1 A - C4 T 1 B DIST= 1.99
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 814 0 40 1822
Refinement
*PLUS
Highest resolution: 2.5 Å / Num. reflection obs: 7578 / σ(I): 1.5 / Rfactor obs: 0.187 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.010.02
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.73
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg18.215
X-RAY DIFFRACTIONo_plane_restr0.010.02

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