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- PDB-1xsd: Crystal structure of the BlaI repressor in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 1xsd
TitleCrystal structure of the BlaI repressor in complex with DNA
Components
  • 5'-D(P*TP*AP*CP*TP*AP*CP*AP*TP*AP*TP*GP*TP*AP*GP*TP*A)-3'
  • penicillinase repressor
KeywordsTRANSCRIPTION/DNA / winged helix protein / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of gene expression / response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Penicillinase repressor fold / Penicillinase repressor domain / BlaI transcriptional regulatory family / Penicillinase repressor / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Penicillinase repressor / Beta-lactamase repressor
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSafo, M.K. / Ko, T.-P. / Musayev, F.N. / Zhao, Q. / Robinson, H. / Scarsdale, N. / Wang, A.H.-J. / Archer, G.L.
CitationJournal: J.Bacteriol. / Year: 2005
Title: Crystal structures of the BlaI repressor from Staphylococcus aureus and its complex with DNA: insights into transcriptional regulation of the bla and mec operons
Authors: Safo, M.K. / Zhao, Q. / Ko, T.-P. / Musayev, F.N. / Robinson, H. / Scarsdale, N. / Wang, A.H.-J. / Archer, G.L.
History
DepositionOct 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-D(P*TP*AP*CP*TP*AP*CP*AP*TP*AP*TP*GP*TP*AP*GP*TP*A)-3'
A: penicillinase repressor


Theoretical massNumber of molelcules
Total (without water)19,8852
Polymers19,8852
Non-polymers00
Water3,261181
1
B: 5'-D(P*TP*AP*CP*TP*AP*CP*AP*TP*AP*TP*GP*TP*AP*GP*TP*A)-3'
A: penicillinase repressor

B: 5'-D(P*TP*AP*CP*TP*AP*CP*AP*TP*AP*TP*GP*TP*AP*GP*TP*A)-3'
A: penicillinase repressor


Theoretical massNumber of molelcules
Total (without water)39,7694
Polymers39,7694
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Unit cell
Length a, b, c (Å)72.141, 72.141, 243.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-302-

HOH

21B-305-

HOH

31A-301-

HOH

41A-303-

HOH

51A-304-

HOH

Detailsthe second part of the dimer is generated by the two-fold symmetry operator of (-x, -y, z)

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Components

#1: DNA chain 5'-D(P*TP*AP*CP*TP*AP*CP*AP*TP*AP*TP*GP*TP*AP*GP*TP*A)-3' / mec operator DNA


Mass: 4896.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein penicillinase repressor / beta-lactamase repressor


Mass: 14988.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q6UB84, UniProt: P0A042*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 4.3 Å3/Da / Density % sol: 71.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, ethylene glycol, magnesium chloride, sodium HEPES, potasssium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 5, 2004
RadiationMonochromator: CHANNEL-CUT SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 9291 / Num. obs: 9285 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 44
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 4.5 / Num. unique all: 901 / % possible all: 99.8

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Processing

Software
NameClassification
CBASSdata collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OKR

1okr


Resolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The 16 nucleotide DNA model in this structure represents an average of the 32 base-pair DNA used in crystallization. (Used the 32 base-pair DNA of 5'-GACTACATTTGTAGTATATTACAAATGTAGTA-3' and ...Details: The 16 nucleotide DNA model in this structure represents an average of the 32 base-pair DNA used in crystallization. (Used the 32 base-pair DNA of 5'-GACTACATTTGTAGTATATTACAAATGTAGTA-3' and 5'-TACTACATTTGTAATATACTACAAATGTAGTC-3') It contains phosphate groups at both 5' and 3' ends. There are a number of wide solvent channels in this crystal. In the void volume between the protein-DNA complex molecules some spiral densities are modeled as strings of water molecules. These are possibly a result of residuals of the averaged model of the DNA. It is also possible that this void volume may host some DNA molecules with low occupancies.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 496 -RANDOM
Rwork0.23 ---
all0.238 9291 --
obs0.237 9023 97.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 328 0 181 1551
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.7
LS refinement shellResolution: 2.7→2.8 Å
RfactorNum. reflection% reflection
Rfree0.528 34 -
Rwork0.405 --
obs--91 %

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