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- PDB-4mnu: Crystal Structure of Uncharacterized SlyA-like Transcription Regu... -

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Basic information

Entry
Database: PDB / ID: 4mnu
TitleCrystal Structure of Uncharacterized SlyA-like Transcription Regulator from Listeria monocytogenes
ComponentsSlyA-like transcription regulator
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / MarR transcription factor / helix-turn-helix
Function / homology
Function and homology information


DNA-binding transcription factor activity
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
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, Molecular replacement / Resolution: 1.898 Å
AuthorsKim, Y. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Uncharacterized SlyA-like Transcription Regulator from Listeria monocytogenes
Authors: Kim, Y. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SlyA-like transcription regulator
B: SlyA-like transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,08710
Polymers35,3232
Non-polymers7658
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-113 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.155, 84.362, 94.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SlyA-like transcription regulator


Mass: 17661.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo0815 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8Y8S9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5, 30 %(w/v) PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 29672 / Num. obs: 29672 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 29.6 Å2 / Rsym value: 0.063 / Net I/σ(I): 15.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1303 / Rsym value: 0.648 / % possible all: 87.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
MOLREPphasing
PHENIX(phenix.refine: dev_1367)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD, Molecular replacement / Resolution: 1.898→38.542 Å / SU ML: 0.2 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1509 5.1 %random
Rwork0.179 ---
obs0.181 29605 98.53 %-
all-20605 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.2 Å2
Refinement stepCycle: LAST / Resolution: 1.898→38.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 41 264 2740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072588
X-RAY DIFFRACTIONf_angle_d1.0643485
X-RAY DIFFRACTIONf_dihedral_angle_d14.6231026
X-RAY DIFFRACTIONf_chiral_restr0.066394
X-RAY DIFFRACTIONf_plane_restr0.004441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8975-1.95880.3081190.26722261238089
1.9588-2.02880.24571280.22482508263698
2.0288-2.110.28011360.196325652701100
2.11-2.2060.26591440.188825532697100
2.206-2.32230.1931390.185325482687100
2.3223-2.46780.22261370.18525682705100
2.4678-2.65830.20541390.186325812720100
2.6583-2.92570.26881510.195425812732100
2.9257-3.34890.20311420.18225942736100
3.3489-4.21840.2081420.153226522794100
4.2184-38.550.20151320.16592685271797
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)
15.5621-0.7983-0.86891.83130.62974.2114-0.2298-0.06090.614-0.02770.11480.232-0.0241-0.46620.11680.2211-0.0202-0.05340.22840.04690.37330.640249.737722.2477
23.8676-2.2173-5.25768.84010.06749.2578-0.28951.241-0.3727-0.68920.03610.11070.2465-0.44860.26090.2925-0.0614-0.00570.254-0.00170.207445.431137.285315.3215
33.61161.1907-0.35533.9527-1.62545.5382-0.1613-0.04230.40160.05990.1870.1772-0.4017-0.0705-0.08550.20410.00930.01040.10140.00290.175342.954434.100129.4678
42.6966-2.80130.56393.3322-1.16342.1318-0.217-0.5254-0.4994-0.52710.52131.27350.4056-0.7881-0.2970.2753-0.0267-0.04350.34870.09820.328833.233132.293531.8478
52.4664-1.1551-2.74076.65671.12625.1803-0.34410.673-1.4823-0.4004-0.10210.71560.6976-0.94040.2830.3042-0.0934-0.02070.3216-0.05690.305237.70727.010521.5072
63.40561.4211-2.34337.9979-5.59034.53180.09150.3452-0.1781-0.0643-0.3331-0.22680.1451-0.07270.20770.3279-0.03260.05440.083-0.02410.231747.218925.12525.014
73.34850.8837-0.15724.2298-0.6231.4274-0.081-0.0460.26180.23140.02140.2806-0.0337-0.07760.02650.16690.00150.01380.1369-0.02820.114945.76538.02628.6938
88.15532.4985-0.88843.88270.24922.14640.2391-2.3950.43191.147-0.0687-0.77480.030.3294-0.0340.28780.0621-0.09130.9643-0.17310.473329.641848.160136.4316
91.60380.08580.06133.1493-2.22072.8695-0.1285-1.397-0.4017-0.15070.09820.4228-0.1195-0.8687-0.22960.37240.01880.03480.65220.1280.53214.631236.646233.6844
104.17330.27650.67060.62680.03511.7913-0.1537-0.0496-0.002-0.09150.0607-0.22620.01620.16640.09090.20980.00190.0340.1950.01790.233525.189242.860122.8604
114.02560.73363.26581.86-1.17818.4622-0.34571.06170.8709-0.1892-0.174-0.29520.06221.18730.34850.2857-0.02730.01560.34950.12710.270126.217749.42168.5855
122.33262.5872-1.03655.8061.78215.7969-0.15112.0609-1.5788-0.20580.32-10.88260.42440.0510.40050.05950.10190.4354-0.0840.393124.589737.22677.6618
131.6266-0.3173-2.74580.2989-0.71835.0356-0.14580.19550.0803-0.12580.14320.05290.22990.0605-0.0080.2495-0.0530.00690.21790.030.198415.536145.331411.2245
147.02971.5104-3.45861.99590.10454.23820.1887-0.39451.4561-0.1215-0.05520.4554-0.5054-0.2018-0.19240.27970.0642-0.05890.3203-0.05280.637834.376756.290123.1672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 31 )
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 46 )
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 57 )
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 70 )
6X-RAY DIFFRACTION6chain 'A' and (resid 71 through 77 )
7X-RAY DIFFRACTION7chain 'A' and (resid 78 through 117 )
8X-RAY DIFFRACTION8chain 'A' and (resid 118 through 143 )
9X-RAY DIFFRACTION9chain 'A' and (resid 144 through 150 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 41 )
11X-RAY DIFFRACTION11chain 'B' and (resid 42 through 57 )
12X-RAY DIFFRACTION12chain 'B' and (resid 58 through 70 )
13X-RAY DIFFRACTION13chain 'B' and (resid 71 through 112 )
14X-RAY DIFFRACTION14chain 'B' and (resid 113 through 150 )

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