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- PDB-2d45: Crystal structure of the MecI-mecA repressor-operator complex -

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Basic information

Entry
Database: PDB / ID: 2d45
TitleCrystal structure of the MecI-mecA repressor-operator complex
Components
  • 5'-D(P*TP*AP*CP*TP*AP*CP*AP*TP*AP*TP*GP*TP*AP*GP*TP*A)-3'
  • Methicillin resistance regulatory protein mecI
KeywordsTranscription/DNA / METHICILLIN / B-LACTAM / Oligonucleotide binding domain / dimerization helical domain / repressor / pseudo-dyad DNA / protein-DNA complex / Transcription-DNA COMPLEX
Function / homology
Function and homology information


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) / Methicillin resistance regulatory protein MecI
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsSafo, M.K. / Ko, T.-P. / Musayev, F.N. / Zhao, Q. / Wang, A.H.-J. / Archer, G.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Structure of the MecI repressor from Staphylococcus aureus in complex with the cognate DNA operator of mec.
Authors: Safo, M.K. / Ko, T.P. / Musayev, F.N. / Zhao, Q. / Wang, A.H. / Archer, G.L.
History
DepositionOct 9, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: 5'-D(P*TP*AP*CP*TP*AP*CP*AP*TP*AP*TP*GP*TP*AP*GP*TP*A)-3'
F: 5'-D(P*TP*AP*CP*TP*AP*CP*AP*TP*AP*TP*GP*TP*AP*GP*TP*A)-3'
G: 5'-D(P*TP*AP*CP*TP*AP*CP*AP*TP*AP*TP*GP*TP*AP*GP*TP*A)-3'
H: 5'-D(P*TP*AP*CP*TP*AP*CP*AP*TP*AP*TP*GP*TP*AP*GP*TP*A)-3'
A: Methicillin resistance regulatory protein mecI
B: Methicillin resistance regulatory protein mecI
C: Methicillin resistance regulatory protein mecI
D: Methicillin resistance regulatory protein mecI


Theoretical massNumber of molelcules
Total (without water)79,5838
Polymers79,5838
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.464, 61.464, 419.777
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11D-143-

HOH

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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'


Mass: 4896.216 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
Methicillin resistance regulatory protein mecI


Mass: 14999.583 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mecI / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P68261
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.6 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 24% PEG 400, 150mM magnesium chloride, 80mM Na-HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
124% PEG 40011
2150mM magnesium chloride11
380mM Na-HEPES11
4H2O11
524% PEG 40012
6150mM magnesium chloride12
780mM Na-HEPES12
8H2O12

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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: Jun 25, 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: 3.8→40 Å / Num. all: 9456 / Num. obs: 9437 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 33.9
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.9 / Num. unique all: 917 / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XSD

1xsd


Resolution: 3.8→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 493 -RANDOM
Rwork0.264 ---
all0.267 9392 --
obs0.267 9168 97.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 3.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3958 1166 0 80 5204
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 3.8→3.94 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.308 56 -
Rwork0.326 --
obs--87.2 %

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