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- PDB-1rpe: THE PHAGE 434 OR2/R1-69 COMPLEX AT 2.5 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1rpe
TitleTHE PHAGE 434 OR2/R1-69 COMPLEX AT 2.5 ANGSTROMS RESOLUTION
Components
  • DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*AP*GP*AP*TP*AP*CP*AP*TP*TP*G P*TP*AP*T)-3')
  • DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*TP*GP*TP*AP*TP*CP*TP*TP*GP*T P*TP*TP*G)-3')
  • PROTEIN (434 REPRESSOR)
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 / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / 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
AuthorsShimon, L.J.W. / Harrison, S.C.
CitationJournal: J.Mol.Biol. / Year: 1993
Title: The phage 434 OR2/R1-69 complex at 2.5 A resolution.
Authors: Shimon, L.J. / Harrison, S.C.
History
DepositionMar 24, 1993Deposition site: RCSB / Processing site: RCSB
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
B: DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*TP*GP*TP*AP*TP*CP*TP*TP*GP*T P*TP*TP*G)-3')
A: DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*AP*GP*AP*TP*AP*CP*AP*TP*TP*G P*TP*AP*T)-3')
L: PROTEIN (434 REPRESSOR)
R: PROTEIN (434 REPRESSOR)


Theoretical massNumber of molelcules
Total (without water)27,3844
Polymers27,3844
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.290, 64.290, 27.690
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(*TP*AP*TP*AP*CP*AP*AP*TP*GP*TP*AP*TP*CP*TP*TP*GP*T P*TP*TP*G)-3')


Mass: 6128.986 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*AP*GP*AP*TP*AP*CP*AP*TP*TP*G P*TP*AP*T)-3')


Mass: 6134.032 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 / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 49.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: pH 5.70, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 300011
3NACLSodium chloride11
4MGCL211
5MES11
6[CO(NH3)6]3+11

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 6984

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Processing

SoftwareName: CORELS / Classification: refinement
RefinementResolution: 2.5→5.5 Å / σ(F): 1.5 /
RfactorNum. reflection% reflection
obs0.209 6984 70.2 %
Refinement stepCycle: LAST / Resolution: 2.5→5.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 814 0 36 1818

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