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- PDB-5dd4: Apo structure of transcriptional factor AraR from Bacteroides the... -

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Basic information

Entry
Database: PDB / ID: 5dd4
TitleApo structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI
ComponentsTRANSCRIPTIONAL REGULATOR AraR
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / AraR / DNA binding / TRANSCRIPTIONAL REGULATOR / BACTEROIDES THETAIOTAOMICRON / HELIX-TURN-HELIX MOTIF / NUDIX FOLD
Function / homology
Function and homology information


hydrolase activity / DNA binding
Similarity search - Function
AraR-like, winged helix DNA-binding domain / AraR C-terminal winged HTH domain / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...AraR-like, winged helix DNA-binding domain / AraR C-terminal winged HTH domain / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / 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 / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NUDIX family hydrolase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.56 Å
AuthorsChang, C. / Tesar, C. / Rodionov, D. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: A novel transcriptional regulator of L-arabinose utilization in human gut bacteria.
Authors: Chang, C. / Tesar, C. / Li, X. / Kim, Y. / Rodionov, D.A. / Joachimiak, A.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATOR AraR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7433
Polymers26,6221
Non-polymers1212
Water48627
1
A: TRANSCRIPTIONAL REGULATOR AraR
hetero molecules

A: TRANSCRIPTIONAL REGULATOR AraR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4866
Polymers53,2442
Non-polymers2424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y,-z+1/21
Buried area3820 Å2
ΔGint-1 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.735, 123.735, 123.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein TRANSCRIPTIONAL REGULATOR AraR / NUDIX family hydrolase


Mass: 26622.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_0354 / Plasmid: PMCSG68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8AAV8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 2.1M Malic Acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2012
RadiationMonochromator: Si(111)double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 10292 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.114 / Χ2: 1.104 / Net I/av σ(I): 21.025 / Net I/σ(I): 10.8 / Num. measured all: 111364
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.56-2.58110.9922730.803100
2.58-2.6110.9142320.846100
2.6-2.6311.10.962700.86100
2.63-2.6510.90.7822590.918100
2.65-2.6811.10.6462420.906100
2.68-2.7110.6872460.887100
2.7-2.73110.5662670.889100
2.73-2.76110.572440.941100
2.76-2.7911.10.4762480.972100
2.79-2.82110.3932700.904100
2.82-2.8511.10.3772450.957100
2.85-2.88110.3552610.964100
2.88-2.9210.90.3372590.98100
2.92-2.9611.20.3182380.998100
2.96-2.9911.10.2712560.981100
2.99-3.0410.90.2632431.102100
3.04-3.0811.10.2132681.07100
3.08-3.1210.90.2242681.164100
3.12-3.1711.10.2022461.127100
3.17-3.23110.1682501.129100
3.23-3.2810.90.1712531.228100
3.28-3.3410.90.1512691.148100
3.34-3.4110.1422461.262100
3.4-3.4710.90.1352661.28100
3.47-3.5510.90.1242551.312100
3.55-3.6310.80.1252551.456100
3.63-3.7210.90.1152511.387100
3.72-3.8210.90.1162641.463100
3.82-3.9410.80.1042641.428100
3.94-4.0610.70.112531.465100
4.06-4.2110.60.1052541.454100
4.21-4.3810.60.0982571.336100
4.38-4.5810.60.0942621.339100
4.58-4.8210.60.0892541.188100
4.82-5.1210.40.0842681.158100
5.12-5.5110.20.0972561.174100
5.51-6.0710.50.0882611.019100
6.07-6.9410.40.0862680.948100
6.94-8.7410.50.0812730.962100
8.74-509.50.0742780.78597.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
SBC-Collectdata collection
RefinementResolution: 2.56→39.16 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.913 / SU B: 16.846 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.438 / ESU R Free: 0.256
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 479 4.8 %RANDOM
Rwork0.1828 ---
obs0.1847 9559 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.01 Å2 / Biso mean: 35.617 Å2 / Biso min: 11.48 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.56→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 8 27 1811
Biso mean--37.23 24.71 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191849
X-RAY DIFFRACTIONr_bond_other_d0.0010.021764
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.9892492
X-RAY DIFFRACTIONr_angle_other_deg0.70934069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29424.78392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67815310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1291510
X-RAY DIFFRACTIONr_chiral_restr0.0710.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02422
LS refinement shellResolution: 2.563→2.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 32 -
Rwork0.243 541 -
all-573 -
obs--73.94 %
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)
110.5504-6.4788-2.65445.32941.34922.1421-0.0843-0.09330.07910.0855-0.0782-0.0968-0.17950.37830.16250.0313-0.0503-0.02030.09560.04490.137359.56657.298732.5131
216.56730.5532-1.96916.9419-0.97674.4514-0.0045-0.34860.168-0.1067-0.1304-0.6239-0.54910.28040.13490.1486-0.0615-0.0530.0370.03530.132157.809221.509730.1694
32.0303-1.3267-0.32235.1013-0.58613.6381-0.0109-0.16270.12030.2353-0.0339-0.2364-0.34290.24110.04480.0865-0.058-0.04220.0646-0.00650.091557.715114.28534.4151
44.2497-2.9045-2.70712.11961.49022.73730.05210.2881-0.4397-0.0735-0.15560.38490.0317-0.27390.10350.0918-0.0466-0.01490.0574-0.04370.256137.453513.243535.9487
55.2733-2.0441-2.79449.99775.26036.8253-0.4153-0.2237-0.4821-0.08060.22890.02960.2175-0.48910.18640.0634-0.05280.05510.2640.05540.256329.905517.279648.0196
618.75410.9378-0.099810.0314-9.83829.709-0.96880.4351-1.4813-0.21241.31090.42010.2905-1.2686-0.34210.8577-0.22180.28790.4808-0.22390.812331.61162.542443.8281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 25
2X-RAY DIFFRACTION2A26 - 39
3X-RAY DIFFRACTION3A40 - 132
4X-RAY DIFFRACTION4A133 - 181
5X-RAY DIFFRACTION5A182 - 218
6X-RAY DIFFRACTION6A219 - 225

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