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- PDB-2wui: Crystal Structure of MexZ, a key repressor responsible for antibi... -

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Basic information

Entry
Database: PDB / ID: 2wui
TitleCrystal Structure of MexZ, a key repressor responsible for antibiotic resistance in Pseudomonas aeruginosa.
ComponentsTRANSCRIPTIONAL REGULATOR
KeywordsTRANSCRIPTION / GENE REGULATION / TRANSCRIPTION REGULATION / TETR / DNA-BINDING
Function / homology
Function and homology information


negative regulation of transmembrane transport / negative regulation of transporter activity / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH-type transcriptional regulator TtgR
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsAlguel, Y. / Lu, D. / Quade, N. / Zhang, X.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Crystal Structure of Mexz, a Key Repressor Responsible for Antibiotic Resistance in Pseudomonas Aeruginosa.
Authors: Alguel, Y. / Lu, D. / Quade, N. / Sauter, S. / Zhang, X.
History
DepositionOct 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATOR


Theoretical massNumber of molelcules
Total (without water)23,7611
Polymers23,7611
Non-polymers00
Water00
1
A: TRANSCRIPTIONAL REGULATOR

A: TRANSCRIPTIONAL REGULATOR


Theoretical massNumber of molelcules
Total (without water)47,5232
Polymers47,5232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2550 Å2
ΔGint-12.4 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.055, 177.055, 54.658
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein TRANSCRIPTIONAL REGULATOR / MEXZ


Mass: 23761.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9RG61

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0000, 0.9791, 0.9793, 0.9757
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97911
30.97931
40.97571
ReflectionResolution: 2.9→88.5 Å / Num. obs: 7354 / % possible obs: 99.5 % / Observed criterion σ(I): 1.43 / Redundancy: 5.7 % / Biso Wilson estimate: 74.37 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.6

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.9→31.384 Å / SU ML: 1.41 / σ(F): 1.43 / Phase error: 37.29 / Stereochemistry target values: ML / Details: B SOL IS 135.431 ACCORDING TO PHENIX OUTPUT.
RfactorNum. reflection% reflection
Rfree0.2768 346 4.7 %
Rwork0.2265 --
obs0.2291 7310 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--84.6823 Å20 Å2-0 Å2
2---84.6823 Å20 Å2
3----32.0298 Å2
Refinement stepCycle: LAST / Resolution: 2.9→31.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1539 0 0 0 1539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091562
X-RAY DIFFRACTIONf_angle_d1.7292111
X-RAY DIFFRACTIONf_dihedral_angle_d21.388582
X-RAY DIFFRACTIONf_chiral_restr0.094235
X-RAY DIFFRACTIONf_plane_restr0.006280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.65290.32961680.25463464X-RAY DIFFRACTION100
3.6529-31.38620.25811780.21613500X-RAY DIFFRACTION99

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