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- PDB-1sax: Three-dimensional structure of s.aureus methicillin-resistance re... -

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Basic information

Entry
Database: PDB / ID: 1sax
TitleThree-dimensional structure of s.aureus methicillin-resistance regulating transcriptional repressor meci in complex with 25-bp ds-DNA
Components
  • 5'-d(CAAAATTACAACTGTAATATCGGAG)-3'
  • 5'-d(GCTCCGATATTACAGTTGTAATTTT)-3'
  • Methicillin resistance regulatory protein mecI
KeywordsTRANSCRIPTION/DNA / winged helix-turn-helix / 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 / Methicillin resistance regulatory protein MecI
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsGarcia-Castellanos, R. / Mallorqui-Fernandez, G. / Marrero, A. / Potempa, J. / Coll, M. / Gomis-Ruth, F.X.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: On the transcriptional regulation of methicillin resistance: MecI repressor in complex with its operator
Authors: Garcia-Castellanos, R. / Mallorqui-Fernandez, G. / Marrero, A. / Potempa, J. / Coll, M. / Gomis-Ruth, F.X.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Three-dimensional structure of MecI. Molecular basis for transcriptional regulation of staphylococcal methicillin resistance
Authors: Garcia-Castellanos, R. / Marrero, A. / Mallorqui-Fernandez, G. / Potempa, J. / Coll, M. / Gomis-Rueth, F.X.
History
DepositionFeb 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-d(GCTCCGATATTACAGTTGTAATTTT)-3'
D: 5'-d(CAAAATTACAACTGTAATATCGGAG)-3'
A: Methicillin resistance regulatory protein mecI
B: Methicillin resistance regulatory protein mecI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0165
Polymers44,9774
Non-polymers391
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.600, 133.600, 54.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-124-

K

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Components

#1: DNA chain 5'-d(GCTCCGATATTACAGTTGTAATTTT)-3'


Mass: 7653.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MecI operator sequence
#2: DNA chain 5'-d(CAAAATTACAACTGTAATATCGGAG)-3'


Mass: 7699.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MecI operator sequence
#3: Protein Methicillin resistance regulatory protein mecI / Methicillin repressor MecI / mecI


Mass: 14812.003 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: N315 / Gene: mecI / Plasmid: pProEX Hta (Invitrogen) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P68262, UniProt: P68261*PLUS
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 8000, magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2MgCl211
3PEG 800012
4MgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9789 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: liq. N2 cooled Si-111 double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.8→39.7 Å / Num. all: 14087 / Num. obs: 13777 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 86.5 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 19.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.3 / % possible all: 93.6

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
AMoREphasing
REFMAC5.1.24refinement
XDSdata reduction
RefinementStarting model: 1OKR

1okr


Resolution: 2.8→39.7 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 16.874 / SU ML: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.501 / ESU R Free: 0.39
RfactorNum. reflection% reflectionSelection details
Rfree0.27601 898 6.5 %RANDOM
Rwork0.21199 ---
all0.21624 13775 --
obs0.21624 12877 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.56 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å2-1.05 Å20 Å2
2---2.1 Å20 Å2
3---3.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 1019 1 37 3089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223260
X-RAY DIFFRACTIONr_angle_refined_deg1.9382.3734561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5125238
X-RAY DIFFRACTIONr_chiral_restr0.0970.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022310
X-RAY DIFFRACTIONr_nbd_refined0.2230.21457
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.240
X-RAY DIFFRACTIONr_mcbond_it0.7651.51196
X-RAY DIFFRACTIONr_mcangle_it1.48821946
X-RAY DIFFRACTIONr_scbond_it1.61332064
X-RAY DIFFRACTIONr_scangle_it2.5394.52615
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.441 68
Rwork0.358 888

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