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- PDB-4l9t: Crystal structure of MepR F27L mutant from multidrug resistant S.... -

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Basic information

Entry
Database: PDB / ID: 4l9t
TitleCrystal structure of MepR F27L mutant from multidrug resistant S. aureus clinical isolate
ComponentsMepR
KeywordsTRANSCRIPTION / winged helix-turn-helix / wHTH / transcription repressor
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
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
MarR family regulatory protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 Å
AuthorsBirukou, I. / Brennan, R.G.
CitationJournal: MBio / Year: 2013
Title: The molecular mechanisms of allosteric mutations impairing MepR repressor function in multidrug-resistant strains of Staphylococcus aureus.
Authors: Birukou, I. / Tonthat, N.K. / Seo, S.M. / Schindler, B.D. / Kaatz, G.W. / Brennan, R.G.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
A: MepR
B: MepR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1664
Polymers33,9742
Non-polymers1922
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-58 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.441, 113.122, 49.936
Angle α, β, γ (deg.)90.000, 98.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MepR / MarR family transcription repressor MepR


Mass: 16987.168 Da / Num. of mol.: 2 / Mutation: F27L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mepR / Production host: Escherichia coli (E. coli) / References: UniProt: Q5Y812
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M (NH4)2HPO4, 20% PEG 3350, pH 8, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 28, 2012
RadiationMonochromator: Si 111. Rosenbaum-Rock double-crystal monochromator: Water cooled, sagittal focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→25 Å / Num. all: 33107 / Num. obs: 32048 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
SERGUIcontrol programdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX(Phaser)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.794→24.72 Å / Occupancy max: 2 / Occupancy min: 0.06 / SU ML: 0.19 / σ(F): 0 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2034 1928 6.24 %
Rwork0.1696 --
obs0.1717 30922 92.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.94 Å2 / Biso mean: 38.2818 Å2 / Biso min: 14.99 Å2
Refinement stepCycle: LAST / Resolution: 1.794→24.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 10 197 2380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072381
X-RAY DIFFRACTIONf_angle_d0.8943239
X-RAY DIFFRACTIONf_chiral_restr0.061367
X-RAY DIFFRACTIONf_plane_restr0.004430
X-RAY DIFFRACTIONf_dihedral_angle_d14.35901
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.794-1.83890.355850.27961195128055
1.8389-1.88860.3171100.25021685179575
1.8886-1.94410.28471220.22041938206088
1.9441-2.00690.2661460.2022111225794
2.0069-2.07860.22851380.16932121225996
2.0786-2.16170.1981470.17312212235998
2.1617-2.260.20151440.16552171231598
2.26-2.37910.18741470.16952198234599
2.3791-2.5280.21381470.17462213236099
2.528-2.7230.1981470.17072211235899
2.723-2.99660.21211480.173322182366100
2.9966-3.42920.19081480.166122232371100
3.4292-4.31670.17371490.146322342383100
4.3167-24.720.20041500.16872264241499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.64010.0122-0.084.46644.95144.80040.0603-0.0022-0.25520.63170.6023-1.35990.5230.4413-0.73740.30740.053-0.02990.3188-0.06510.3814-2.021-30.6699-15.805
24.991.81590.0783.6607-0.18453.73490.2373-0.1094-0.12060.0257-0.06390.44660.0146-0.3893-0.1540.1543-0.0213-0.02180.162-0.00890.2227-15.735-16.9673-1.2511
36.7114-4.19093.73876.36090.70024.68680.458-0.6311-0.9292-1.554-0.14180.91171.6587-0.0502-0.36670.6648-0.01640.00670.34210.14970.2814-17.6882-22.79198.4049
49.86365.5242-6.53045.7006-5.17215.1524-0.087-0.5955-0.11221.03-0.2779-0.33770.11920.85230.44540.31910.0446-0.01920.2691-0.00590.209-9.03-14.5668.3774
55.8973-3.5469-3.80956.1962.47995.9929-0.145-1.03590.07690.56090.2964-0.275-0.00570.664-0.06130.1263-0.0025-0.04970.27180.0050.1915-14.9331-7.23224.8234
65.8051-3.5859-3.87326.6391.94842.7623-0.7565-0.2722-0.94180.90920.23850.64910.5536-0.92980.42880.24740.00180.03680.46650.06840.2463-23.4654-9.3839.8364
71.0257-2.9373-2.81427.34035.72566.99870.1120.19070.0897-0.4867-0.1267-0.07260.1219-0.2308-0.01120.25080.00870.00430.26310.01270.1864-10.2787-18.312-17.3139
82.77042.776-0.98647.3243-1.40194.67640.20040.4117-0.0293-0.3843-0.05180.2916-0.2879-0.5889-0.15220.33750.0556-0.0190.32850.1030.3265-14.6592-38.0375-27.5416
91.62230.2243-0.13514.6177-6.48347.4779-0.01690.16210.4250.58080.68490.8325-0.6864-0.5854-0.67730.29720.06290.05180.29920.09210.3414-14.1311-41.8942-13.4178
106.01181.08311.48531.85780.79671.507-0.0663-0.02990.2929-0.00590.0128-0.1692-0.12280.1070.03750.2136-0.02280.00030.20570.030.2651-1.937-53.46351.5197
116.8339-3.3139-1.54165.5164-0.14450.58710.0446-0.74020.7048-0.3501-0.1221-0.1414-2.00370.0537-0.01240.720.12990.01230.3762-0.19880.46491.8476-49.644810.9259
125.2033-3.25621.21113.6606-1.13835.251-0.5112-0.970.10250.64430.58060.152-0.6515-0.3156-0.04520.26890.06870.02310.3076-0.00860.2483-0.4757-60.278211.5559
133.2065-3.49124.69298.7607-7.11759.46480.20750.25270.0815-0.5725-0.13420.0253-0.0990.3673-0.13250.2610.02340.02610.2463-0.02210.2771-6.5038-54.4444-13.7255
146.11893.56233.44873.42674.54128.57440.18840.7072-0.2764-0.98430.2624-0.59090.80410.8328-0.3560.5390.0903-0.01250.321-0.08120.2322-3.6585-37.5156-28.8955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 49 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 60 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 73 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 81 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 82 through 94 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 95 through 118 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 119 through 140 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 26 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 27 through 46 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 47 through 60 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 61 through 94 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 95 through 118 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 119 through 139 )B0

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