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- PDB-1myk: CRYSTAL STRUCTURE, FOLDING, AND OPERATOR BINDING OF THE HYPERSTAB... -

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Basic information

Entry
Database: PDB / ID: 1myk
TitleCRYSTAL STRUCTURE, FOLDING, AND OPERATOR BINDING OF THE HYPERSTABLE ARC REPRESSOR MUTANT PL8
ComponentsARC REPRESSOR
KeywordsTRANSCRIPTION REGULATION
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Arc-like DNA binding domain / Arc-like DNA binding domain / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional repressor arc
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsSchildbach, J.F. / Milla, M.E. / Jeffrey, P.D. / Raumann, B.E. / Sauer, R.T.
Citation
Journal: Biochemistry / Year: 1995
Title: Crystal structure, folding, and operator binding of the hyperstable Arc repressor mutant PL8.
Authors: Schildbach, J.F. / Milla, M.E. / Jeffrey, P.D. / Raumann, B.E. / Sauer, R.T.
#1: Journal: Nature / Year: 1994
Title: DNA Recognition by Beta-Sheets in the Arc Repressor-Operator Crystal Structure
Authors: Raumann, B.E. / Rould, M.A. / Pabo, C.O. / Sauer, R.T.
History
DepositionOct 12, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARC REPRESSOR
B: ARC REPRESSOR


Theoretical massNumber of molelcules
Total (without water)12,5092
Polymers12,5092
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-23 kcal/mol
Surface area5450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.800, 51.800, 110.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ARC REPRESSOR


Mass: 6254.315 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / Gene: MUTATED ARC GENE / Plasmid: PTA200-PL8 / Production host: Escherichia coli (E. coli) / References: UniProt: P03050
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPL8 IS HYPERSTABLE RELATIVE TO ARC, BUT HAS REDUCED AFFINITY FOR DNA. PL8 DIMER IS 2.5 KCALMOL MORE ...PL8 IS HYPERSTABLE RELATIVE TO ARC, BUT HAS REDUCED AFFINITY FOR DNA. PL8 DIMER IS 2.5 KCALMOL MORE STABLE THAN WILD TYPE DIMER BY THERMAL OR CHEMICAL DENATURATION. DNA AFFINITY IS DOWN 5.0 KCALMOL FOR REACTION OF TWO DIMERS BINDING ARC OPERATOR. ARC AND PL8 ARE DIMERIC IN SOLUTION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
230 mMbis-tris propane-HCl1drop
31 mM1dropNaN3
422-24 %PEG34001dropprecipitant
57-9 %2-propanol1dropprecipitant
6100 mMNaHEPES1dropprecipitant
7precipitant1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 5340 / % possible obs: 90.4 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 6 Å / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 56.6 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.277 --
Rwork0.217 --
obs0.217 5340 90.4 %
Displacement parametersBiso mean: 33.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms764 0 0 16 780
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.49
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.99
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.52
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it4.152.5
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 5340 / Rfactor obs: 0.217 / Rfactor Rfree: 0.277
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.49

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