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- PDB-2bv6: Crystal structure of MgrA, a global regulator and major virulence... -

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Basic information

Entry
Database: PDB / ID: 2bv6
TitleCrystal structure of MgrA, a global regulator and major virulence determinant in Staphylococcus aureus
ComponentsHTH-TYPE TRANSCRIPTIONAL REGULATOR MGRA
KeywordsTRANSCRIPTIONAL REGULATOR / MULTIDRUG RESISTANCE REGULATOR / VIRULENCE DETERMINANT / TRANSCRIPTIONAL FACTORS
Function / homology
Function and homology information


: / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / 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 ...Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / 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
HTH-type transcriptional regulator MgrA / HTH-type transcriptional regulator MgrA
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsChen, P.R. / Bae, T. / Williams, W.A. / Duguid, E.M. / Rice, P.A. / Schneewind, O. / He, C.
CitationJournal: Nat.Chem.Biol. / Year: 2006
Title: An Oxidation-Sensing Mechanism is Used by the Global Regulator Mgra in Staphylococcus Aureus.
Authors: Chen, P.R. / Bae, T. / Williams, W.A. / Duguid, E.M. / Rice, P.A. / Schneewind, O. / He, C.
History
DepositionJun 22, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-TYPE TRANSCRIPTIONAL REGULATOR MGRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6302
Polymers16,5341
Non-polymers961
Water1629
1
A: HTH-TYPE TRANSCRIPTIONAL REGULATOR MGRA
hetero molecules

A: HTH-TYPE TRANSCRIPTIONAL REGULATOR MGRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2594
Polymers33,0672
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)119.800, 119.800, 62.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein HTH-TYPE TRANSCRIPTIONAL REGULATOR MGRA / MGRA


Mass: 16533.510 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: NEWMAN / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7X448, UniProt: P0C1S0*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 5-143 OF THE 147 RESIDUE PROTEIN WITH N-TERMINAL GLY SER HIS CLONING ARTIFACTS.

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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: 3.9 Å3/Da / Density % sol: 70 %
Crystal growpH: 6.6
Details: PROTEIN WAS CRYSTALLIZED FROM 1.6 M AMMONIUM SULFATE, 0.1M MES, PH 6.0, XTALS WERE RINSED IN CRYOPROTECTANT SOLUTIONS CONSISTING OF RESERVOIR BUFFER WITH AN ADDED 10%, 20% AND 25% GLYCEROL ...Details: PROTEIN WAS CRYSTALLIZED FROM 1.6 M AMMONIUM SULFATE, 0.1M MES, PH 6.0, XTALS WERE RINSED IN CRYOPROTECTANT SOLUTIONS CONSISTING OF RESERVOIR BUFFER WITH AN ADDED 10%, 20% AND 25% GLYCEROL RESPECTIVELY. SELENOMETHIONINE (SEMET)-CONTAINING PROTEIN WAS CRYSTALLIZED UNDER THE SAME CONDITION.

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.5
DetectorDetector: CCD / Date: Apr 3, 2005 / Details: BENT MIRROR
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.8→24.5 Å / Num. obs: 8544 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 19.3 % / Biso Wilson estimate: 118.1 Å2 / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 10 % / Rmerge(I) obs: 0.95 / % possible all: 98

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→24.39 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 287948.87 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.292 337 5.1 %RANDOM
Rwork0.25 ---
obs0.25 6560 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.404 Å2 / ksol: 0.31802 e/Å3
Displacement parametersBiso mean: 80.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.87 Å212.88 Å20 Å2
2--4.87 Å20 Å2
3----9.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.8→24.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 5 9 1132
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.081.5
X-RAY DIFFRACTIONc_mcangle_it3.682
X-RAY DIFFRACTIONc_scbond_it4.32
X-RAY DIFFRACTIONc_scangle_it6.82.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.063 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.451 52 5.3 %
Rwork0.472 926 -
obs--87 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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