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- PDB-3mqq: The Crystal Structure of the PAS domain in complex with Ethanol o... -

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Basic information

Entry
Database: PDB / ID: 3mqq
TitleThe Crystal Structure of the PAS domain in complex with Ethanol of a Transcriptional Regulator in the LuxR family from Burkholderia thailandensis to 1.65A
ComponentsTranscriptional regulator, LuxR familyTranscriptional regulation
KeywordsTranscription regulator / PAS domain / LuxR / regulator / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / PAS domain / PAS domain / Beta-Lactamase / PAS domain ...LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / PAS domain / PAS domain / Beta-Lactamase / PAS domain / PAS domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHANOL / Transcriptional regulator, LuxR family
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsStein, A.J. / Tesar, C. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of the PAS domain in complex with Ethanol of a Transcriptional Regulator in the LuxR family from Burkholderia thailandensis to 1.65A
Authors: Stein, A.J. / Tesar, C. / Buck, K. / Joachimiak, A.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, LuxR family
B: Transcriptional regulator, LuxR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,37911
Polymers26,9622
Non-polymers4169
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-25 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.438, 35.726, 66.986
Angle α, β, γ (deg.)90.000, 91.490, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Transcriptional regulator, LuxR family / Transcriptional regulation


Mass: 13481.028 Da / Num. of mol.: 2 / Fragment: sequence database residues 2-121
Source method: isolated from a genetically manipulated source
Details: pMCSG7 / Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I2609 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2SVC5
#2: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.6 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% ethanol, 20% PEG 4000, 0.1M Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2010
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 32890 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.085 / Χ2: 2.372 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.713.70.62732440.931199
1.71-1.783.70.45532500.959199
1.78-1.863.70.29732701.025199.3
1.86-1.963.70.21132481.207199.5
1.96-2.083.70.14732921.441199.5
2.08-2.243.70.11333201.832199.7
2.24-2.463.70.09732702.334199.9
2.46-2.823.70.09233323.3811100
2.82-3.553.60.07433414.248199.7
3.55-503.50.07233236.664196.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.65→33.48 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.915 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1667 5.1 %RANDOM
Rwork0.224 ---
obs0.225 32814 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.769 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20.16 Å2
2--0.3 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 26 68 1895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221887
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9542553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9425241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.86921.59188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26215301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7791523
X-RAY DIFFRACTIONr_chiral_restr0.1010.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211443
X-RAY DIFFRACTIONr_mcbond_it0.61.51167
X-RAY DIFFRACTIONr_mcangle_it0.9421869
X-RAY DIFFRACTIONr_scbond_it1.9843720
X-RAY DIFFRACTIONr_scangle_it2.744.5678
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 114 -
Rwork0.296 2238 -
all-2352 -
obs--96.39 %
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)
110.3245-10.13213.180424.97070.52688.35230.39740.0031-0.5681-0.4146-0.41541.53770.144-0.5470.01810.0949-0.06720.00470.3316-0.00670.22965.5456-19.306718.3361
219.12671.0052-0.817411.31991.93750.2101-0.2657-0.2984-0.275-0.15770.20960.23380.0578-0.03090.05610.1503-0.1602-0.03770.2997-0.00170.066113.9492-21.366318.0098
31.2574-3.54640.870511.65382.56179.86830.0069-0.0048-0.0018-0.0528-0.09670.08750.0576-0.20220.08980.0224-0.0237-0.00420.1368-0.0170.053619.643-15.449820.8678
44.1478-0.471-0.111915.27060.53658.71450.0425-0.54680.39760.4124-0.22870.2982-0.3533-0.18770.18620.08030.0009-0.00680.1727-0.04010.057424.4956-9.93429.7634
56.8596-0.8471-2.76912.66635.022212.97820.0771-0.2689-0.27570.4005-0.1977-0.12250.4559-0.44740.12070.0493-0.0235-0.00170.12670.0070.060519.1317-20.450923.73
612.2766-3.73231.67241.4954-1.33941.8745-0.3546-0.2864-0.591-0.06450.0596-0.07860.3036-0.01880.29490.1820.01480.05430.04170.02860.259627.05-24.480920.0024
72.1663-8.6291-3.567830.15683.172715.4517-0.20380.0616-0.0440.6107-0.3037-0.3760.3561-0.2730.50750.2162-0.0404-0.04440.27170.05030.152123.6153-24.714527.9396
813.59788.8426-5.83676.3271-6.071510.68650.17670.0972-0.51140.05060.0605-0.20340.3284-0.0791-0.23710.1272-0.0187-0.00390.1523-0.01090.081525.8922-17.172229.8261
97.9897-3.3931-7.745110.03756.193812.4258-0.2383-0.2971-0.00520.24360.0299-0.22930.39860.4730.20840.07670.0035-0.01570.17370.0160.095934.2323-15.947524.8612
106.1888-0.55050.167715.6072-0.1739-0.515-0.33190.01470.58810.02340.2935-0.5360.0040.07580.03840.03720.023-0.00020.42130.00360.184638.6112-9.959124.4397
1116.9831.64352.907739.09650.7083-1.35360.44610.19050.8875-0.8603-0.60320.12230.06270.10970.15720.1518-0.0438-0.0190.31360.02780.282833.8129-3.876420.0746
122.09574.1224-4.492518.2337-3.967311.2561-0.03040.0166-0.11990.1078-0.0134-0.32030.17-0.02690.04380.12430.026-0.02330.1296-0.00120.292727.21471.702418.6357
1315.3292-17.9068-5.549720.71176.57943.79540.08650.28170.5125-0.1372-0.2919-0.554-0.4860.02090.20530.1506-0.0266-0.01580.1060.02480.239326.1508-3.59314.1562
142.30851.889-0.80854.8264-3.36173.34160.0064-0.2864-0.04520.64250.0215-0.0632-0.21650.0466-0.02790.21210.076-0.00980.18310.01380.137834.1402-17.549217.2234
1511.5762-2.123-1.73439.1097-5.944115.5809-0.0581-0.1714-0.7942-0.3224-0.4094-0.54331.12340.52080.46760.14360.04980.00650.1132-0.00820.234436.1033-23.993618.8463
167.9278-4.1285-1.90624.24961.42763.43050.03690.12550.1519-0.0586-0.130.0938-0.12160.0410.09310.0208-0.01610.02230.09820.01340.085124.7997-9.093616.4596
170.30590.2795-1.007414.256-5.088710.1055-0.0679-0.13250.20010.0404-0.0059-0.2448-0.405-0.08220.07380.12250.0274-0.08210.1716-0.09010.259123.09540.526723.8508
185.5244-4.845-3.99053.96572.61739.3704-0.09950.03680.1960.0528-0.0498-0.16510.1695-0.03390.14920.0146-0.01370.01140.1058-0.06510.119620.9146-9.780420.7649
1910.6855-0.6386-2.803116.7481-3.78767.71090.06730.7394-0.5216-0.8774-0.1302-0.33050.49260.45120.06290.07020.02910.0220.1821-0.02120.100628.1431-19.957311.9814
204.14561.8002-0.10189.4345-3.86114.69230.0216-0.49760.32890.62930.16310.4326-0.2666-0.3866-0.18470.1010.01310.04170.2462-0.01210.10159.962-11.314422.034
213.65360.916-0.43298.70015.520810.46710.0978-0.26540.35550.28820.0631-0.08320.0171-0.0251-0.16080.0377-0.0110.01380.10660.00220.068913.4792-10.038313.5606
223.5093-0.95752.06927.52064.652518.45980.1912-0.1185-0.4618-0.161-0.14890.45850.6057-0.7507-0.04230.1122-0.0444-0.03810.15440.01750.12024.0155-21.15055.704
238.77633.08286.34338.63755.89329.81170.184-0.35370.01630.3786-0.20260.33950.0666-0.73810.01860.0354-0.00180.01070.17230.00550.08823.2222-15.20938.0732
246.50472.5691-7.7118.0711-3.912121.42280.2949-0.16260.699-0.2645-0.2842-0.3038-0.455-0.1842-0.01080.08810.0060.02570.0611-0.01750.173611.6291-6.30388.668
253.7541-2.419-4.78833.16623.24847.78480.06060.32190.345-0.0851-0.04840.026-0.2974-0.2896-0.01220.22140.02090.00470.08360.05650.216711.4782-4.7192.18
2618.70468.15423.691834.88922.35845.52560.2436-0.49830.58590.1477-0.35120.3447-0.402-0.35820.10760.08020.0349-0.03310.1478-0.02810.13733.0425-7.33875.9744
279.9298-3.8562-4.11147.3059-0.55069.9506-0.19810.24520.1351-0.1059-0.1441-0.07070.22250.03480.34220.0697-0.0004-0.04580.1418-0.00580.09014.3516-14.8666-0.6707
2814.46754.60110.6168.2572-0.094410.49180.1056-0.18520.2487-0.21770.04390.4902-0.08340.0362-0.14940.05440.00550.01810.13230.0080.132410.5411-14.2203-5.4051
297.7014-3.4891-4.87938.45520.71867.3051-0.20320.32650.1251-0.3760.2903-0.2460.63020.1263-0.08710.169-0.0183-0.00750.22640.00640.128511.0455-20.632-8.814
30-0.33521.25465.670443.9118-6.108832.75670.44860.25420.02950.1811-0.58680.40181.72480.57110.13820.58850.3116-0.03250.4552-0.09440.126213.5633-26.7117-2.868
3110.120.13015.41668.535-1.386911.41760.3104-0.07940.029-0.4393-0.0621-0.5220.26810.5753-0.24830.33620.0422-0.00670.17580.01910.220416.6932-32.10124.3738
3211.515913.968-7.226538.7369-25.726417.6310.42790.2911-0.2081-0.7425-0.13010.34230.79790.3463-0.29780.26640.12880.06040.2466-0.020.081419.5947-23.2983.7915
3313.2922-9.33311.33249.91322.66895.23270.35240.1162-0.6658-0.1775-0.40130.99440.0658-0.20670.04890.16410.00920.0230.1818-0.03490.254415.8771-11.539-3.6753
346.3778-0.36851.13761.18630.41147.1132-0.0230.19670.293-0.20280.01570.1211-0.60740.1580.00740.1515-0.03190.02510.11370.01150.079718.1419-9.4165-3.1601
358.03062.6283-3.13274.8762-3.3454.79990.2336-0.1679-0.29210.1405-0.10220.04020.4206-0.0292-0.13150.1653-0.0308-0.01450.0853-0.00740.077112.9213-25.06859.8161
360.5320.6534-0.26611.49771.80653.83690.03750.0446-0.2063-0.1158-0.0462-0.18040.0282-0.10910.00870.406-0.024-0.12760.1084-0.00130.19258.5859-29.61996.8879
378.09326.735-3.97458.519-4.2926.0038-0.12690.17290.1669-0.18520.1073-0.0765-0.00070.09780.01970.0578-0.0110.03750.0984-0.01260.062817.6717-13.67885.8456
381.5131-2.68795.260120.4674-7.822317.3859-0.31130.11210.21290.7983-0.2625-0.3605-0.91430.36250.57380.1169-0.02340.0620.24430.00020.258432.1914-7.1068.5861
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 8
2X-RAY DIFFRACTION2A9 - 14
3X-RAY DIFFRACTION3A15 - 20
4X-RAY DIFFRACTION4A21 - 25
5X-RAY DIFFRACTION5A26 - 31
6X-RAY DIFFRACTION6A32 - 37
7X-RAY DIFFRACTION7A38 - 43
8X-RAY DIFFRACTION8A44 - 48
9X-RAY DIFFRACTION9A49 - 53
10X-RAY DIFFRACTION10A54 - 60
11X-RAY DIFFRACTION11A61 - 65
12X-RAY DIFFRACTION12A66 - 71
13X-RAY DIFFRACTION13A72 - 77
14X-RAY DIFFRACTION14A78 - 83
15X-RAY DIFFRACTION15A84 - 89
16X-RAY DIFFRACTION16A90 - 99
17X-RAY DIFFRACTION17A100 - 105
18X-RAY DIFFRACTION18A106 - 110
19X-RAY DIFFRACTION19A111 - 116
20X-RAY DIFFRACTION20B4 - 10
21X-RAY DIFFRACTION21B11 - 18
22X-RAY DIFFRACTION22B19 - 23
23X-RAY DIFFRACTION23B24 - 28
24X-RAY DIFFRACTION24B29 - 34
25X-RAY DIFFRACTION25B35 - 39
26X-RAY DIFFRACTION26B40 - 44
27X-RAY DIFFRACTION27B45 - 49
28X-RAY DIFFRACTION28B50 - 54
29X-RAY DIFFRACTION29B55 - 60
30X-RAY DIFFRACTION30B61 - 66
31X-RAY DIFFRACTION31B67 - 72
32X-RAY DIFFRACTION32B73 - 78
33X-RAY DIFFRACTION33B79 - 83
34X-RAY DIFFRACTION34B84 - 92
35X-RAY DIFFRACTION35B93 - 99
36X-RAY DIFFRACTION36B100 - 107
37X-RAY DIFFRACTION37B108 - 116
38X-RAY DIFFRACTION38B117 - 121

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