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- PDB-6cmv: Crystal structure of Archaeal Biofilm Regulator (AbfR2) from Sulf... -

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Basic information

Entry
Database: PDB / ID: 6cmv
TitleCrystal structure of Archaeal Biofilm Regulator (AbfR2) from Sulfolobus acidocaldarius
ComponentsTranscriptional regulator Lrs14-like protein
KeywordsGENE REGULATION / wHTH / Archaea / biofilm
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Transcription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulator Lrs14-like protein / Transcriptional regulator Lrs14-like protein
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsEssen, L.-O. / Vogt, M.S. / Banerjee, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Sonderforschungsbereich (SFB)987 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Crystal structure of an Lrs14-like archaeal biofilm regulator from Sulfolobus acidocaldarius.
Authors: Marian S Vogt / Simon L Völpel / Sonja Verena Albers / Lars Oliver Essen / Ankan Banerjee /
Abstract: The small winged helix-turn-helix (wHTH) proteins of the Lrs14 family are major transcriptional regulators and act as archaeal biofilm regulators (AbfRs) in the crenarchaeote Sulfolobus ...The small winged helix-turn-helix (wHTH) proteins of the Lrs14 family are major transcriptional regulators and act as archaeal biofilm regulators (AbfRs) in the crenarchaeote Sulfolobus acidocaldarius. Here, the first crystal structure of an AbfR ortholog, AbfR2, the deletion of which is known to impair biofilm formation, is presented. Like most other wHTH orthologs, AbfR2 is dimeric in solution as well as in its 2.45 Å resolution crystal structure. Given the presence of three independent AbfR2 dimers in the asymmetric unit, the crystal structure shows a considerable degree of conformational variation within the dimer, the antiparallel orientations of which are stabilized by coiled-coil interaction between H4 helices. Conserved anchor interactions between helices H0 and H4 of AbfR2 further contribute to dimer stabilization. The combined structural and bioinformatic analysis reveals cluster-specific structural differences between different members of the Lrs14 protein family.
History
DepositionMar 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator Lrs14-like protein
B: Transcriptional regulator Lrs14-like protein
C: Transcriptional regulator Lrs14-like protein
D: Transcriptional regulator Lrs14-like protein
E: Transcriptional regulator Lrs14-like protein
F: Transcriptional regulator Lrs14-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,16424
Polymers99,2196
Non-polymers1,94518
Water2,864159
1
A: Transcriptional regulator Lrs14-like protein
B: Transcriptional regulator Lrs14-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8229
Polymers33,0732
Non-polymers7497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-68 kcal/mol
Surface area13670 Å2
MethodPISA
2
C: Transcriptional regulator Lrs14-like protein
D: Transcriptional regulator Lrs14-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8229
Polymers33,0732
Non-polymers7497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-75 kcal/mol
Surface area13330 Å2
MethodPISA
3
E: Transcriptional regulator Lrs14-like protein
F: Transcriptional regulator Lrs14-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5206
Polymers33,0732
Non-polymers4474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-61 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.859, 94.314, 78.909
Angle α, β, γ (deg.)90.00, 112.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transcriptional regulator Lrs14-like protein


Mass: 16536.510 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: ATY89_00385, ATZ20_03430 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U3FE21, UniProt: Q4J9G1*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: mother liquor: 45% (v/v) MPD, 0.1 M Bicine (pH 9) mixed 1:1 with 13.5 mg/mL protein in 300 mM NaCl, 20 mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→47.16 Å / Num. obs: 36289 / % possible obs: 99.4 % / Redundancy: 2 % / Biso Wilson estimate: 60 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.03478 / Rrim(I) all: 0.04919 / Net I/σ(I): 14.87
Reflection shellResolution: 2.45→2.538 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3555 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3595 / CC1/2: 0.647 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→47.157 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 1734 4.78 %Random selection
Rwork0.1659 ---
obs0.1684 36287 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60 Å2
Refinement stepCycle: LAST / Resolution: 2.45→47.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5588 0 130 159 5877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095766
X-RAY DIFFRACTIONf_angle_d1.1237687
X-RAY DIFFRACTIONf_dihedral_angle_d16.1252302
X-RAY DIFFRACTIONf_chiral_restr0.057855
X-RAY DIFFRACTIONf_plane_restr0.004942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4501-2.52220.34041430.26422862X-RAY DIFFRACTION99
2.5222-2.60360.30191270.24262855X-RAY DIFFRACTION99
2.6036-2.69660.30361480.2362877X-RAY DIFFRACTION99
2.6966-2.80460.23551260.21862874X-RAY DIFFRACTION99
2.8046-2.93220.25991490.19822860X-RAY DIFFRACTION99
2.9322-3.08680.23361370.17462844X-RAY DIFFRACTION99
3.0868-3.28010.2331450.17512904X-RAY DIFFRACTION99
3.2801-3.53330.20291280.15422868X-RAY DIFFRACTION99
3.5333-3.88870.20451720.1512870X-RAY DIFFRACTION100
3.8887-4.4510.20111650.14022868X-RAY DIFFRACTION100
4.451-5.60640.18651390.14692926X-RAY DIFFRACTION100
5.6064-47.16570.21351550.16742945X-RAY DIFFRACTION100
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)
11.54490.9446-0.43850.5695-0.33251.0013-0.0891-0.33350.2156-0.22190.13621.19720.2868-0.972-0.00010.5123-0.042-0.03580.6037-0.00440.78550.154744.999544.704
22.48220.29332.43632.25610.75532.452-0.1763-0.297-0.3605-0.09290.21350.45580.4006-0.396900.5543-0.01650.08810.5736-0.06920.630711.718636.166541.7095
32.2213-3.18640.18744.0397-0.50170.0568-0.1073-0.26670.59080.13060.3538-0.47680.1526-0.11810.0560.3453-0.02310.04320.5475-0.04830.61710.855152.566145.2042
42.98124.2186-1.59786.0337-2.14061.0744-0.60160.98010.4262-1.42030.9865-0.2603-0.6903-0.7050.17190.73310.170.12520.917-0.24210.9235-6.285261.254336.617
50.638-0.30120.86780.3565-0.17191.43330.29790.9372-0.28530.1632-0.1603-0.07890.04710.54950.00120.4102-0.004-0.02760.63270.03540.6939-17.333266.567236.8816
61.40010.92050.69941.90111.44081.079-0.07960.2322-0.2825-0.72110.0022-0.5578-0.3065-0.1145-0.00120.4657-0.03960.0740.4987-0.02840.6509-26.980563.352334.4392
70.48680.1587-0.18151.1056-1.02481.0648-0.2776-0.02710.3406-0.3030.29820.18430.1042-0.266900.440.02170.01960.43870.00950.6084-31.545870.745542.2108
82.4098-3.14071.21074.0016-1.7111.1029-0.5934-0.8934-0.09260.74450.95560.89260.0541-0.5683-0.03210.48770.02850.08680.6659-0.02550.7518-5.892759.375753.7162
90.8048-0.3-0.16550.73620.67190.5918-0.1767-0.55540.0148-0.2215-0.29451.3919-0.8788-2.0024-0.00160.89260.07630.01310.9165-0.06910.688432.617331.8124.0849
101.4984-1.2395-0.40932.1480.14022.69110.192-0.2508-0.31140.2742-0.09350.10350.51250.133-00.646-0.01860.02880.4945-0.02610.459641.243726.6864-9.8607
111.09460.1862-0.17070.48630.44941.0218-0.12520.11550.0283-0.36870.4682-0.4530.28770.6717-00.82590.0690.08630.6802-0.04090.686644.314336.148118.492
122.084-0.7574-0.16921.8909-0.64441.3080.10080.6370.3022-1.3392-0.24980.3669-0.36380.0069-0.02220.7350.070.03730.56-0.00740.451631.549349.605425.3196
131.7185-1.2575-0.74551.03210.27940.90120.05170.60840.0326-1.1045-0.22350.3222-0.4067-0.6529-0.00920.68820.0505-0.07770.47020.04720.559721.660156.048630.4933
140.994-1.4279-1.32762.51472.70532.5882-0.3286-0.0443-0.15110.49370.03560.23010.4355-0.0172-0.00140.5746-0.02110.08210.4555-0.00390.446330.226241.067231.3937
159.28455.6181-0.48494.964-3.40196.1928-0.03320.1202-0.6614-0.4168-0.5115-1.23771.09111.8884-1.79360.66260.0593-0.32860.68830.04770.49441.021229.836770.3366
162.0928-1.18520.8450.7025-0.86715.3705-0.5868-1.00151.10021.02330.5712-1.5961-0.99721.87470.52630.51010.0327-0.19270.7964-0.05660.89138.80432.779860.6464
172.79360.5639-0.63041.1416-0.2340.8203-0.73980.38291.42030.42610.0171-0.3641-0.33720.3568-0.180.56560.0702-0.0730.628-0.00640.872235.667336.660350.7541
180.3171-0.22480.01550.53940.36850.3749-0.13310.4148-0.6431-0.3393-0.4254-1.20141.67520.379-0.00010.67630.07190.00850.6858-0.07930.665637.162725.134653.056
190.61310.81130.08561.05750.09970.02740.11780.13430.2135-0.082-0.1023-0.16650.99650.4305-00.55160.06920.00390.5215-0.10310.476926.864126.994253.9273
201.38370.6080.31090.97641.50456.03630.43120.328-0.5760.43880.06320.17391.6929-0.30360.08350.63680.0391-0.07240.6295-0.09480.677527.544628.221644.783
211.95521.64410.82542.3248-0.81893.36510.5567-0.5122-0.32320.31490.393-0.07890.2558-0.41243.65160.64320.052-0.29150.5424-0.10260.435632.50120.610977.8274
220.50480.06380.6360.51650.45611.06560.48871.4985-0.1284-1.034-0.40150.79910.06110.25530.00090.83630.147-0.22840.8495-0.06320.658149.906417.663580.2352
231.598-0.4473-1.81780.65430.24732.17990.09480.4355-0.2293-0.938-0.22430.11920.6899-0.288500.6918-0.0089-0.04990.68630.0050.523261.471615.54388.3817
240.87440.1934-0.8050.4149-0.15930.7382-0.37810.57751.0490.108-0.4805-0.30790.30410.2895-0.00010.5750.0147-0.11080.46960.03180.528556.661520.774696.7638
254.005-3.21561.52392.5921-1.0273.6201-0.5270.50661.39980.287-0.4081-2.4931-0.86251.093-1.3030.4332-0.01330.00430.61040.08850.829872.313819.7006102.5068
262.2445-0.83521.55860.1413-0.45280.8545-0.334-0.2963-0.3580.21070.22010.2355-0.2072-0.3172-0.49940.4740.0705-0.07360.4578-0.12650.448740.716426.683785.6105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 122 )
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 20 )
5X-RAY DIFFRACTION5chain 'B' and (resid 21 through 44 )
6X-RAY DIFFRACTION6chain 'B' and (resid 45 through 68 )
7X-RAY DIFFRACTION7chain 'B' and (resid 69 through 93 )
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 123 )
9X-RAY DIFFRACTION9chain 'C' and (resid 12 through 38 )
10X-RAY DIFFRACTION10chain 'C' and (resid 39 through 93 )
11X-RAY DIFFRACTION11chain 'C' and (resid 94 through 123 )
12X-RAY DIFFRACTION12chain 'D' and (resid 12 through 44 )
13X-RAY DIFFRACTION13chain 'D' and (resid 45 through 68 )
14X-RAY DIFFRACTION14chain 'D' and (resid 69 through 122 )
15X-RAY DIFFRACTION15chain 'E' and (resid 12 through 23 )
16X-RAY DIFFRACTION16chain 'E' and (resid 24 through 37 )
17X-RAY DIFFRACTION17chain 'E' and (resid 38 through 55 )
18X-RAY DIFFRACTION18chain 'E' and (resid 56 through 68 )
19X-RAY DIFFRACTION19chain 'E' and (resid 69 through 78 )
20X-RAY DIFFRACTION20chain 'E' and (resid 79 through 93 )
21X-RAY DIFFRACTION21chain 'E' and (resid 94 through 122 )
22X-RAY DIFFRACTION22chain 'F' and (resid 12 through 37 )
23X-RAY DIFFRACTION23chain 'F' and (resid 38 through 68 )
24X-RAY DIFFRACTION24chain 'F' and (resid 69 through 78 )
25X-RAY DIFFRACTION25chain 'F' and (resid 79 through 86 )
26X-RAY DIFFRACTION26chain 'F' and (resid 87 through 122 )

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