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- PDB-1sd6: Crystal Structure of Native MecI at 2.65 A -

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Basic information

Entry
Database: PDB / ID: 1sd6
TitleCrystal Structure of Native MecI at 2.65 A
ComponentsMethicillin resistance regulatory protein mecI
KeywordsDNA BINDING PROTEIN / BlaI / MecI / repressor / methicillin / B-lactam
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
Methicillin resistance regulatory protein MecI
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.65 Å
AuthorsSafo, M.K. / Zhao, Q. / Musayev, F.N. / Robinson, H. / Scarsdale, N. / 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
DepositionFeb 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
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

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Assembly

Deposited unit
A: Methicillin resistance regulatory protein mecI
B: Methicillin resistance regulatory protein mecI


Theoretical massNumber of molelcules
Total (without water)29,6522
Polymers29,6522
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-23 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.711, 72.748, 73.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains the biological homodimer

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Components

#1: Protein Methicillin resistance regulatory protein mecI / MECI


Mass: 14826.030 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: MECI, SA0040 / Plasmid: pET3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P68262
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Sodium Cacodylate, Magnesium acetate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMpotassium phosphate1reservoirpH7.6
2200 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 12, 2001 / Details: mirrors
RadiationMonochromator: MSC Confocal Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→36.48 Å / Num. all: 9536 / Num. obs: 9418 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.2
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1180 / % possible all: 88.4

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Processing

Software
NameVersionClassification
CNS1refinement
bioteXdata reduction
bioteXdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.65→32.61 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 91660.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 439 4.7 %RANDOM
Rwork0.207 ---
all0.216 9536 --
obs0.207 9347 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.1141 Å2 / ksol: 0.311292 e/Å3
Displacement parametersBiso mean: 71.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.14 Å20 Å20 Å2
2--1.65 Å20 Å2
3----5.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.65→32.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 0 59 2069
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 77 5.4 %
Rwork0.348 1353 -
obs-1430 85 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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