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- PDB-1lli: THE CRYSTAL STRUCTURE OF A MUTANT PROTEIN WITH ALTERED BUT IMPROV... -

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Basic information

Entry
Database: PDB / ID: 1lli
TitleTHE CRYSTAL STRUCTURE OF A MUTANT PROTEIN WITH ALTERED BUT IMPROVED HYDROPHOBIC CORE PACKING
Components
  • DNA (5'-D(*AP*AP*TP*AP*CP*CP*AP*CP*TP*GP*GP*CP*GP*GP*TP*GP*A P*TP*AP*T)-3')
  • DNA (5'-D(*TP*AP*TP*AP*TP*CP*AP*CP*CP*GP*CP*CP*AP*GP*TP*GP*G P*TP*AP*T)-3')
  • PROTEIN (LAMBDA REPRESSOR)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


maintenance of viral latency / latency-replication decision / positive regulation of viral transcription / negative regulation of transcription by competitive promoter binding / core promoter sequence-specific DNA binding / identical protein binding
Similarity search - Function
: / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / 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 ...: / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / 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 speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsLim, W.A. / Hodel, A. / Sauer, R.T. / Richards, F.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: The crystal structure of a mutant protein with altered but improved hydrophobic core packing.
Authors: Lim, W.A. / Hodel, A. / Sauer, R.T. / Richards, F.M.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Refined 1.8 Angstrom Crystal Structure of the Lambda Repressor-Operator Complex
Authors: Beamer, L.J. / Pabo, C.O.
History
DepositionMar 25, 1994Deposition site: BNL / Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*AP*AP*TP*AP*CP*CP*AP*CP*TP*GP*GP*CP*GP*GP*TP*GP*A P*TP*AP*T)-3')
E: DNA (5'-D(*TP*AP*TP*AP*TP*CP*AP*CP*CP*GP*CP*CP*AP*GP*TP*GP*G P*TP*AP*T)-3')
A: PROTEIN (LAMBDA REPRESSOR)
B: PROTEIN (LAMBDA REPRESSOR)


Theoretical massNumber of molelcules
Total (without water)32,5604
Polymers32,5604
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.150, 68.900, 56.790
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6158.004 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*AP*TP*AP*TP*CP*AP*CP*CP*GP*CP*CP*AP*GP*TP*GP*G P*TP*AP*T)-3')


Mass: 6108.967 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (LAMBDA REPRESSOR)


Mass: 10146.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Production host: Escherichia coli (E. coli) / Keywords: MUTANT V36L,M40L,V47I / References: UniProt: P03034
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Details: Jordan, S.R. et al.(1985). Science, 230, 1383-1385.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(v/v)PEG4001drop
220 %(v/v)PEG4001reservoir

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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: 2.1 Å / Lowest resolution: 8 Å / % possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge F obs: 0.196
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.4 Å / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.261

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.1→8 Å /
Rfactor% reflection
Rwork0.196 -
obs0.196 99.7 %
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1396 814 0 92 2302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3

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