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- PDB-3mqo: The Crystal Structure of the PAS domain in complex with isopropan... -

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Basic information

Entry
Database: PDB / ID: 3mqo
TitleThe Crystal Structure of the PAS domain in complex with isopropanol of a Transcriptional Regulator in the LuxR family from Burkholderia thailandensis to 1.7A
ComponentsTranscriptional regulator, LuxR family
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
ISOPROPYL ALCOHOL / Transcriptional regulator, LuxR family
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 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 isopropanol of a Transcriptional Regulator in the LuxR family from Burkholderia thailandensis to 1.7A
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)27,43710
Polymers26,9622
Non-polymers4758
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-28 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.615, 35.746, 67.096
Angle α, β, γ (deg.)90.000, 91.990, 90.000
Int Tables number3
Space group name H-MP121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transcriptional regulator, LuxR family


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

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Non-polymers , 5 types, 95 molecules

#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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, sitting drop / pH: 5.6
Details: 20% Iso-propanol, 20% PEG 4000, 0.1M Sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING 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 12, 2010
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 29569 / % possible obs: 97.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 / Χ2: 1.854 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.763.70.45828720.638196.3
1.76-1.833.80.33428970.689196.6
1.83-1.913.80.25329380.911196.8
1.91-2.023.80.17929111.045197
2.02-2.143.80.13629441.577197.4
2.14-2.313.80.10529741.632197.5
2.31-2.543.80.08529741.83198
2.54-2.913.80.07129962.51198.3
2.91-3.663.70.05630232.918198.5
3.66-503.50.05630404.936195.9

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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
HKL-3000phasing
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementResolution: 1.7→31.54 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.239 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1483 5 %RANDOM
Rwork0.225 ---
obs0.226 29569 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.929 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.06 Å2
2---0.06 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 30 87 1914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221885
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.9592556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7175241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.88521.95487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14515298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2931521
X-RAY DIFFRACTIONr_chiral_restr0.0890.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211437
X-RAY DIFFRACTIONr_mcbond_it0.4581.51164
X-RAY DIFFRACTIONr_mcangle_it0.7121868
X-RAY DIFFRACTIONr_scbond_it1.63721
X-RAY DIFFRACTIONr_scangle_it2.1524.5682
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 112 -
Rwork0.29 1972 -
all-2084 -
obs--95.68 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
110.7668-1.8607-0.069118.01867.1386-4.83020.0114-0.1864-0.0579-0.0345-0.09860.69380.3-0.28460.08720.1258-0.03870.01380.37260.03620.15066.314618.006919.4761
217.65716.0077-0.585517.22292.28510.131-0.2925-0.1849-0.2567-0.48730.17880.59580.1356-0.29120.11370.0756-0.0425-0.03780.22930.02650.024715.617616.606417.097
310.18156.2287.38548.60185.74059.4767-0.1655-0.64240.44640.151-0.02990.3228-0.3191-0.45550.19550.040.03150.00810.1638-0.01530.042320.359126.030226.3275
48.25387.44241.051611.30771.20241.8574-0.0488-0.27640.66340.2491-0.04940.3579-0.1025-0.23380.09830.09370.0272-0.00140.1853-0.02470.024922.922324.351228.4909
57.837-5.9631-0.97859.38551.38846.4784-0.0311-0.0478-0.39060.0114-0.1025-0.34420.4902-0.01040.13360.0788-0.01860.02650.09120.01660.074520.869214.377321.0853
69.41181.5347-0.52464.9708-8.590911.0992-0.11050.0577-0.6742-0.0416-0.0024-0.12210.36010.17840.11290.1280.02020.02830.05170.02060.212928.060411.992220.644
71.99043.4614-3.077735.910716.648611.7044-0.1753-0.133-0.33670.66950.1762-0.55990.7012-0.3193-0.00090.1337-0.0209-0.02140.18140.05690.102223.488614.667129.817
81.5543.20880.97551.6888-1.399112.4405-0.0885-0.1723-0.1093-0.0303-0.231-0.28120.23290.33780.31950.0748-0.00510.00430.12760.01980.100530.221921.535228.6595
95.14952.93955.35613.74017.37635.2157-0.0569-0.07110.08280.5390.0146-0.47380.23070.17080.04230.05670.01530.01430.1840.0660.08936.319222.538924.4075
1013.86592.1545-6.23514.3917-7.67038.5996-0.07680.10920.27710.16390.1117-0.1874-0.1440.6194-0.0350.056-0.0191-0.02840.2062-0.00930.17938.074428.564823.9505
1118.2516-15.0297-2.14114.9623-5.67787.5409-0.2185-0.19240.98460.4572-0.0567-0.5646-0.58240.38670.27520.1273-0.0236-0.09470.087-0.00120.33332.968733.878920.7196
123.0341-8.39583.160514.6092-0.71660.1582-0.04050.20720.43020.10130.048-1.0087-0.0463-0.1235-0.00750.18040.0059-0.04130.14750.0110.300426.476739.336816.3778
132.4087-5.9666-2.4499.4493.24844.386-0.15760.14750.0890.0736-0.0684-0.0244-0.17170.15790.2260.055-0.01080.01090.13110.03960.147827.604630.60313.5179
142.090.7107-0.44285.661-5.83745.79790.088-0.1333-0.29150.8295-0.4237-0.3361-0.36160.35390.33570.24530.0236-0.00860.13850.03360.153234.567217.418619.4384
159.2332-3.68463.45777.7659-4.2846.97770.01840.383-0.6434-0.107-0.1637-0.4940.51590.32350.14540.05540.03930.04250.1669-0.01140.16735.702716.434415.565
169.08-5.4808-4.64699.30764.80295.5376-0.00170.15090.0606-0.19-0.2720.3355-0.3531-0.15130.27370.04170.008-0.00910.08050.01310.05722.085429.367816.6085
17-0.89342.0524-0.600616.933-6.75131.7988-0.06220.1050.1660.41860.1006-0.238-0.1998-0.2258-0.03840.16430.0436-0.08910.1385-0.04910.231722.565538.691423.1064
180.22612.70840.12031.0079-2.92884.4763-0.2315-0.15730.29850.0736-0.16420.1538-0.3505-0.07820.39570.04020.0348-0.01980.1271-0.05890.108321.38928.285521.4215
1910.2871-0.0125-1.032214.04830.639916.0782-0.05720.7213-0.4963-0.46190.0433-0.51670.89030.4160.01390.050.01920.02720.1653-0.02540.074128.139917.055112.1855
202.10932.53333.34773.4797-1.00074.4341-0.0966-0.20980.26070.86790.14520.5849-0.2028-0.2374-0.04860.20990.05940.05050.3623-0.02460.12499.928926.230423.187
217.23284.346-0.4766.5817-0.482814.89390.1-0.36520.07650.1950.10860.0286-0.3635-0.2704-0.20860.04730.0171-0.00020.1194-0.00310.086113.298927.775715.2347
228.90114.02145.71126.12095.85888.63890.2147-0.3874-0.27660.1885-0.24440.23380.385-0.52160.02970.0374-0.01760.01210.12720.02360.07146.415818.54778.589
233.9535-0.25790.061412.583512.260316.804-0.1157-0.2631-0.14150.43310.00580.550.741-0.28430.10990.0232-0.0150.00670.12420.04840.07414.056719.65555.4522
246.01862.1074-3.27611.5745-5.850210.80670.2082-0.13320.4557-0.11340.02660.0257-0.2449-0.0855-0.23480.08250.00950.0360.0716-0.01880.094911.072430.03438.6527
254.8223-0.6668-0.93375.32790.8543.87680.04480.14870.2432-0.2006-0.04310.0403-0.1068-0.0486-0.00170.1278-0.00620.01420.05760.0130.08811.455132.08562.0267
2615.7754.67566.996131.21356.7384-0.3919-0.056-0.35180.58260.3714-0.17390.7389-0.2138-0.28060.22990.05190.02280.0090.1388-0.0170.10862.969929.45395.936
2710.8419-4.8312.22066.72583.53741.44220.25250.4048-0.1978-0.2396-0.0738-0.04890.06250.0969-0.17880.05-0.0086-0.00120.13360.00040.05194.54722.1212-0.7099
285.51193.4717-1.761610.6072-0.53437.9529-0.03790.39880.1029-0.330.18580.40050.0095-0.0817-0.14790.02650.02080.00330.13740.01760.073410.070721.1963-7.28
296.9601-10.3403-8.449915.8857-1.303712.1292-0.11990.7801-0.4781-0.2470.02350.04640.1351-0.38830.09630.134-0.00290.01830.3-0.07470.068111.754415.3125-7.6307
309.4785-9.6374-0.397916.8897-13.746527.58480.42410.4498-0.2399-0.0197-0.12780.16760.9194-0.2336-0.29630.28770.0352-0.04520.1563-0.06550.107713.907510.1961-2.8728
314.1335-2.45167.27938.2711-1.50754.98480.19020.0513-0.0986-0.25140.02010.10280.19560.5202-0.21020.22090.0506-0.01290.23170.00670.151816.89484.75394.3664
324.66871.4871-2.8196.9778-6.15575.90870.30320.1224-0.05260.00190.00540.20620.15390.3531-0.30860.10620.07720.00370.2009-0.03550.079719.751913.47194.1826
335.9586-6.6407-1.57675.3622.02720.06310.07820.1579-0.2962-0.0798-0.22280.5209-0.0229-0.05090.14460.1320.0050.01990.1874-0.00380.090315.938725.381-3.7857
348.6704-3.23240.66723.7943-0.30755.54450.09470.33320.5252-0.309-0.0198-0.0235-0.42340.1268-0.07490.094-0.03260.02850.12540.01060.079917.617928.6074-4.6138
358.16965.0892-3.53147.3569-4.22064.13310.1015-0.1667-0.23110.0161-0.1617-0.13770.18330.01950.06020.08760.01620.01530.079-0.01510.031914.637413.37048.903
362.056-3.78365.358810.7705-4.55743.92450.37650.0628-0.2166-0.5675-0.2130.44770.43180.1486-0.16360.1926-0.0143-0.02460.10250.01990.12149.30766.02016.144
3712.74924.8584-0.83325.66951.88322.06080.2618-0.2274-0.0618-0.0452-0.15580.26560.2273-0.0233-0.1060.1017-0.0089-0.02880.07590.01490.066111.523216.4439.0307
3815.70535.9578-1.362513.7388-3.95318.7863-0.26010.41850.1884-0.15250.1031-0.2936-0.19470.34750.1570.0261-0.0040.02830.12860.00250.03120.45826.68283.7104
397.039-11.695415.17218.0851-15.285330.969-0.72920.52440.26570.22210.05970.3074-0.82820.88230.66940.1284-0.05810.10930.36040.03630.271231.682829.70997.2372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 8
2X-RAY DIFFRACTION2A9 - 16
3X-RAY DIFFRACTION3A17 - 22
4X-RAY DIFFRACTION4A23 - 27
5X-RAY DIFFRACTION5A28 - 33
6X-RAY DIFFRACTION6A34 - 38
7X-RAY DIFFRACTION7A39 - 45
8X-RAY DIFFRACTION8A46 - 50
9X-RAY DIFFRACTION9A51 - 55
10X-RAY DIFFRACTION10A56 - 60
11X-RAY DIFFRACTION11A61 - 66
12X-RAY DIFFRACTION12A67 - 72
13X-RAY DIFFRACTION13A73 - 78
14X-RAY DIFFRACTION14A79 - 85
15X-RAY DIFFRACTION15A86 - 91
16X-RAY DIFFRACTION16A92 - 98
17X-RAY DIFFRACTION17A99 - 104
18X-RAY DIFFRACTION18A105 - 110
19X-RAY DIFFRACTION19A111 - 116
20X-RAY DIFFRACTION20B4 - 9
21X-RAY DIFFRACTION21B10 - 15
22X-RAY DIFFRACTION22B16 - 22
23X-RAY DIFFRACTION23B23 - 27
24X-RAY DIFFRACTION24B28 - 34
25X-RAY DIFFRACTION25B35 - 39
26X-RAY DIFFRACTION26B40 - 44
27X-RAY DIFFRACTION27B45 - 49
28X-RAY DIFFRACTION28B50 - 56
29X-RAY DIFFRACTION29B57 - 60
30X-RAY DIFFRACTION30B61 - 66
31X-RAY DIFFRACTION31B67 - 72
32X-RAY DIFFRACTION32B73 - 78
33X-RAY DIFFRACTION33B79 - 83
34X-RAY DIFFRACTION34B84 - 91
35X-RAY DIFFRACTION35B92 - 99
36X-RAY DIFFRACTION36B100 - 105
37X-RAY DIFFRACTION37B106 - 110
38X-RAY DIFFRACTION38B111 - 115
39X-RAY DIFFRACTION39B116 - 121

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