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- PDB-3tb6: Structure of the effector-binding domain of arabinose repressor A... -

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Basic information

Entry
Database: PDB / ID: 3tb6
TitleStructure of the effector-binding domain of arabinose repressor AraR from Bacillus subtilis
ComponentsArabinose metabolism transcriptional repressor
KeywordsDNA BINDING PROTEIN / transcription regulation / arabinose binding
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Arabinose metabolism transcriptional repressor, ligand-binding domain / Transcriptional regulator LacI/GalR-like, sensor domain / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Periplasmic binding protein-like domain / Response regulator / Periplasmic binding protein-like I / Winged helix DNA-binding domain superfamily ...Arabinose metabolism transcriptional repressor, ligand-binding domain / Transcriptional regulator LacI/GalR-like, sensor domain / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Periplasmic binding protein-like domain / Response regulator / Periplasmic binding protein-like I / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-L-arabinopyranose / Arabinose metabolism transcriptional repressor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsRezacova, P. / Prochazkova, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of the effector-binding domain of the arabinose repressor AraR from Bacillus subtilis.
Authors: Prochazkova, K. / Cermakova, K. / Pachl, P. / Sieglova, I. / Fabry, M. / Otwinowski, Z. / Rezacova, P.
History
DepositionAug 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arabinose metabolism transcriptional repressor
B: Arabinose metabolism transcriptional repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2656
Polymers66,7812
Non-polymers4844
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-13 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.068, 106.333, 111.847
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 Arabinose metabolism transcriptional repressor


Mass: 33390.270 Da / Num. of mol.: 2 / Fragment: effector binding domain (UNP residues 71-362)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: araC, araR, BSU33970, yvbS / Plasmid: pET51/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P96711
#2: Sugar ChemComp-ARB / beta-L-arabinopyranose / beta-L-arabinose / L-arabinose / arabinose / Arabinose


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArapbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-arabinopyranoseCOMMON NAMEGMML 1.0
b-L-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: arabinose 50mM at 16.8mg/ml, 70mM HEPES pH7.5, 7% PEG8000, 6% ethylene glycol, 20% glycerol, 10mM spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.917 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 27, 2011
Details: double crystal monochromator with 2 sets of Rh-coated mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 38046 / Num. obs: 33024 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 66 % / Rmerge(I) obs: 0.57 / Net I/σ(I): 35.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.9 / % possible all: 59.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.3.0037refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JFT

1jft


Resolution: 2.21→29.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 13.192 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23099 1660 5 %RANDOM
Rwork0.1857 ---
obs0.18808 31295 86.74 %-
all-36080 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.952 Å2
Baniso -1Baniso -2Baniso -3
1-9.13 Å20 Å20 Å2
2---5.41 Å20 Å2
3----3.71 Å2
Refinement stepCycle: LAST / Resolution: 2.21→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4459 0 32 245 4736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224658
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9866305
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78325.074203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52515885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2051521
X-RAY DIFFRACTIONr_chiral_restr0.0960.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023423
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.22241
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23165
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4511.52963
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.73724666
X-RAY DIFFRACTIONr_scbond_it1.27631884
X-RAY DIFFRACTIONr_scangle_it1.954.51625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.21→2.263 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 89 -
Rwork0.262 1472 -
obs--56.97 %
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)
14.2807-3.0479-2.77479.44464.36629.61870.0974-0.17470.24530.0859-0.21050.4477-0.4960.30940.1131-0.3264-0.0264-0.0344-0.2078-0.0431-0.1225-4.3647.34926.146
23.8502-2.4213-0.58937.75640.70752.8986-0.0436-0.06920.34550.8155-0.13840.1339-0.28170.13350.182-0.2848-0.04670.0115-0.1386-0.0589-0.0751-5.517.06931.771
33.0313-3.0001-0.64697.2503-0.59322.9322-0.0439-0.27660.18051.00640.0060.57560.0819-0.16310.0378-0.159-0.02460.1284-0.0976-0.05710.0034-12.229-1.20334.71
40.92860.758-0.14043.88011.79314.3696-0.04430.1392-0.0184-0.3946-0.11510.5140.627-0.34430.1593-0.20830.0019-0.0655-0.08560.0018-0.0744-9.341-13.6218.44
54.0133-0.93940.001520.839915.510814.6755-0.12090.04530.06380.22630.4257-0.70170.34770.728-0.3049-0.13220.03460.0283-0.14130.066-0.12512.651-15.06216.501
64.0912-1.4491-2.07756.0687-0.13668.2596-0.0397-0.0742-0.1546-0.3625-0.02-0.84330.1980.91560.0597-0.18830.02170.0398-0.04010.0043-0.07086.41-10.8635.907
718.065304.497617.6267024.25110.50430.17570.782-1.98350.2137-1.6986-1.81561.4843-0.7180.1514-0.08260.05680.0486-0.01530.01251.0034.4036.996
81.5449-2.1811-3.93274.87145.661410.5020.18170.30990.2573-0.2319-0.31840.5327-0.5919-0.56770.1366-0.28730.0932-0.0838-0.0575-0.02580.038-12.6656.19117.923
91.83670.0481-3.13283.28833.20649.87260.1060.33450.18730.0551-0.55281.0877-0.3684-1.52870.4469-0.22070.1674-0.06270.1197-0.07750.3149-19.6894.27520.079
1018.73276.22610.943727.13545.778218.748-0.68052.3642-0.1191-2.99970.67330.2905-0.96381.88180.00730.20590.0219-0.07510.1782-0.0164-0.1364-1.98-7.118-6.701
112.43021.7594-2.48543.69570.17384.14940.110.15580.0155-0.0968-0.1101-0.01390.0225-0.02960.0002-0.23880.0273-0.029-0.2061-0.0224-0.1654.3115.35227.272
121.4988-0.4541.56385.7083-1.22683.02110.1124-0.0188-0.2040.221-0.14120.22120.2266-0.13950.0287-0.2291-0.0350.0234-0.15960.0014-0.1193.30314.60533.394
132.9079-3.47110.84539.4896-0.25843.7634-0.1389-0.1971-0.09560.73920.060.11350.1403-0.00410.079-0.1581-0.0345-0.0149-0.1612-0.0062-0.15157.07722.99839.426
140.6203-0.0528-0.69624.5512-0.82661.6365-0.02840.18090.0631-0.8442-0.1389-0.696-0.15970.22010.1672-0.040.01160.1346-0.03370.0246-0.011115.27631.22917.218
155.83761.8844-2.51346.9908-2.30283.33430.08130.1440.4486-0.9007-0.0893-0.6842-0.12350.27350.00790.07630.0320.1803-0.0540.0149-0.046814.66939.41114.358
1610.3654-1.6036-6.335612.0738-2.590413.7160.1720.63460.5649-1.29950.20521.1746-1.0067-1.3909-0.37730.48190.1239-0.28410.1842-0.00110.0369-0.11338.3567.601
176.5085-2.28244.14938.9764-0.186213.87750.0690.7267-0.0043-1.9948-0.09250.9621-0.3119-1.0730.02350.5590.0632-0.04280.09980.0153-0.0393.29528.575.459
180.6366-1.00161.04288.2678-7.069912.23770.20130.2763-0.2305-1.44120.0303-0.06090.7782-0.2357-0.2317-0.02060.06230.09780.0094-0.0035-0.056812.27218.82715.326
192.03481.14680.01815.7604-4.143711.4513-0.06850.3140.0239-0.5437-0.4505-0.8827-0.46591.13790.5191-0.0060.15110.2023-0.0573-0.01640.073619.54520.69320.396
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 98
2X-RAY DIFFRACTION2A99 - 130
3X-RAY DIFFRACTION3A131 - 181
4X-RAY DIFFRACTION4A182 - 234
5X-RAY DIFFRACTION5A235 - 246
6X-RAY DIFFRACTION6A247 - 300
7X-RAY DIFFRACTION7A301 - 311
8X-RAY DIFFRACTION8A312 - 333
9X-RAY DIFFRACTION9A334 - 354
10X-RAY DIFFRACTION10A355 - 361
11X-RAY DIFFRACTION11B80 - 97
12X-RAY DIFFRACTION12B98 - 130
13X-RAY DIFFRACTION13B131 - 175
14X-RAY DIFFRACTION14B176 - 216
15X-RAY DIFFRACTION15B217 - 243
16X-RAY DIFFRACTION16B244 - 267
17X-RAY DIFFRACTION17B268 - 291
18X-RAY DIFFRACTION18B292 - 333
19X-RAY DIFFRACTION19B334 - 362

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