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- PDB-7kci: DETERMINANTS OF REPRESSOR/OPERATOR RECOGNITION FROM THE STRUCTURE... -

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Basic information

Entry
Database: PDB / ID: 7kci
TitleDETERMINANTS OF REPRESSOR/OPERATOR RECOGNITION FROM THE STRUCTURE OF THE TRP OPERATOR BINDING SITE
ComponentsSelf-complementary deoxyoligonucleotide decamer d(CCACTAGTGG)
KeywordsDNA / B-DNA / DOUBLE HELIX / DEOXYRIBONUCLEIC ACID
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsShakked, Z. / Guzikevich-Guerstein, G. / Frolow, F. / Rabinovich, D. / Joachimiak, A. / Sigler, P.B.
Funding support3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Israel Science Foundation
United States - Israel Binational Science Foundation (BSF)
CitationJournal: Nature / Year: 1994
Title: Determinants of repressor/operator recognition from the structure of the trp operator binding site.
Authors: Shakked, Z. / Guzikevich-Guerstein, G. / Frolow, F. / Rabinovich, D. / Joachimiak, A. / Sigler, P.B.
History
DepositionSep 12, 1994Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Self-complementary deoxyoligonucleotide decamer d(CCACTAGTGG)
B: Self-complementary deoxyoligonucleotide decamer d(CCACTAGTGG)


Theoretical massNumber of molelcules
Total (without water)6,0902
Polymers6,0902
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-4 kcal/mol
Surface area3840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.900, 32.900, 95.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-149-

HOH

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Components

#1: DNA chain Self-complementary deoxyoligonucleotide decamer d(CCACTAGTGG)


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 49.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7 / Details: PEG 200, NA CACODYLATE, SPERMINE_HCL, MGCL2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→33 Å / Num. obs: 4034 / Redundancy: 2.03 % / Rsym value: 0.087

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Processing

Software
NameClassification
NUCLSQrefinement
ULTIMAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: standard B-DNA model

Resolution: 1.95→6 Å / Cross valid method: THROUGHOUT / σ(F): 2 /
RfactorNum. reflection
obs0.17 3200
Displacement parametersBiso max: 100.9 Å2 / Biso mean: 16.9851 Å2 / Biso min: 2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 121 525
Biso mean---31.96 -
Num. residues----20

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