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- PDB-6qh0: The complex structure of hsRosR-S5 (VNG0258H/RosR-S5) -

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Basic information

Entry
Database: PDB / ID: 6qh0
TitleThe complex structure of hsRosR-S5 (VNG0258H/RosR-S5)
Components
  • (DNA (28-MER)) x 2
  • hsRosR DNA binding protein
KeywordsDNA BINDING PROTEIN / Halophiles / wHTH DNA binding protein / RosR / High salt medium / Protein-DNA interactions
Function / homologyTranscription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / metal ion binding / : / DNA / DNA (> 10) / PadR family transcription regulator RosR
Function and homology information
Biological speciesHalobacterium salinarum NRC-1 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.436 Å
AuthorsShaanan, B. / Kutnowski, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1382/13 Israel
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR.
Authors: Kutnowski, N. / Shmulevich, F. / Davidov, G. / Shahar, A. / Bar-Zvi, D. / Eichler, J. / Zarivach, R. / Shaanan, B.
History
DepositionJan 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: hsRosR DNA binding protein
B: hsRosR DNA binding protein
C: hsRosR DNA binding protein
D: hsRosR DNA binding protein
E: DNA (28-MER)
F: DNA (28-MER)
G: DNA (28-MER)
H: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,62236
Polymers87,1388
Non-polymers2,48428
Water1,63991
1
A: hsRosR DNA binding protein
B: hsRosR DNA binding protein
G: DNA (28-MER)
H: DNA (28-MER)
hetero molecules


  • defined by author
  • Evidence: SAXS, SAXS results indicating that one protein dimer bound a single sequence., gel filtration, The elution volume of the complex indicated that hsRosR binds one DNA molecule as a dimer., ...Evidence: SAXS, SAXS results indicating that one protein dimer bound a single sequence., gel filtration, The elution volume of the complex indicated that hsRosR binds one DNA molecule as a dimer., isothermal titration calorimetry, The binding stoichiometry was approximately one, indicating that one protein dimer bound a single sequence.
  • 44.9 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)44,92819
Polymers43,5694
Non-polymers1,35915
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: hsRosR DNA binding protein
D: hsRosR DNA binding protein
E: DNA (28-MER)
F: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,69417
Polymers43,5694
Non-polymers1,12513
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.545, 83.109, 89.601
Angle α, β, γ (deg.)95.810, 95.500, 105.110
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
hsRosR DNA binding protein


Mass: 13179.443 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: hsRosR DNA binding protein
Source: (gene. exp.) Halobacterium salinarum NRC-1 (Halophile)
Gene: VNG_0258H / Production host: Haloferax volcanii (archaea) / Variant (production host): WR341 / References: UniProt: Q9HSF4

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DNA chain , 2 types, 4 molecules EGFH

#2: DNA chain DNA (28-MER)


Mass: 8678.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA (28-MER) / Source: (synth.) Halobacterium salinarum NRC-1 (Halophile)
#3: DNA chain DNA (28-MER)


Mass: 8531.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA (28-MER) / Source: (synth.) Halobacterium salinarum NRC-1 (Halophile)

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Non-polymers , 3 types, 119 molecules

#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.79 Å3/Da / Density % sol: 67.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The complex crystallized from a buffer containing 20 mM HEPES, pH 7, 2 M KCl and 0.02% azide. Crystals grown with S5 (DNA/hsRosR ratio = 1.7) appeared after 3 days in wells containing 2.4 M ...Details: The complex crystallized from a buffer containing 20 mM HEPES, pH 7, 2 M KCl and 0.02% azide. Crystals grown with S5 (DNA/hsRosR ratio = 1.7) appeared after 3 days in wells containing 2.4 M (NH4)2SO4, 20 mM MnCl2 and 0.02% azide.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.436→44.57 Å / Num. obs: 29262 / % possible obs: 85.9 % / Redundancy: 3.2 % / Rsym value: 0.181 / Net I/σ(I): 4.2
Reflection shellResolution: 2.44→2.73 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The starting model for molecular replacement was VNG0258H/RosR (from KCl; PDB code 6FDH) and a DNA model derived from Mycobacterium tuberculosis MosR (PDB code 4FX4) but with the S5 sequences

6fdh

4fx4


Resolution: 2.436→44.569 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.76
RfactorNum. reflection% reflection
Rfree0.2676 1356 4.93 %
Rwork0.2392 --
obs0.2407 27497 57.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 247.49 Å2 / Biso mean: 59.3866 Å2 / Biso min: 4.04 Å2
Refinement stepCycle: final / Resolution: 2.436→44.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3645 2296 120 91 6152
Biso mean--100.47 27.54 -
Num. residues----567
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4364-2.52350.416150.37511161213
2.5235-2.62450.3197220.396251453611
2.6245-2.74390.3648420.38291035107723
2.7439-2.88860.3786770.34681813189040
2.8886-3.06950.36531400.342583272357
3.0695-3.30640.36231670.29463296346373
3.3064-3.6390.3012130.24973956416987
3.639-4.16530.24542320.22014171440392
4.1653-5.24650.21922340.20044306454094
5.2465-44.57690.22882240.20464351457596
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)
14.5721-1.17980.81160.72470.03670.31270.26370.5192-0.0488-0.2296-0.1671-0.42390.4090.3980.04420.63510.1842-0.27820.60310.20110.5136-17.227116.2005-22.714
23.5029-2.3515-3.24223.24952.14983.2999-0.09920.0079-0.19520.20080.09080.10860.2116-0.19210.0180.17580.0785-0.03510.28710.11420.1707-10.884518.602-11.0356
30.98122.66050.15017.22340.51034.3262-0.0909-0.36350.03430.18940.1648-0.0718-1.05410.25790.01480.32590.05180.01280.18770.08160.2422-3.309320.6093-5.2463
44.6033-1.3413.16090.4029-0.88192.30080.1040.89560.4464-0.65060.06870.1237-0.40380.16720.07240.25350.0819-0.04940.53050.11860.5289-7.282926.5853-16.7534
50.7855-0.80190.14460.9061-0.41220.75550.01330.37490.14790.01270.085-0.0988-0.2238-0.22720.2855-0.02240.1622-0.09160.38540.16690.3884-16.92820.1192-11.5661
66.5757-0.8032-1.1533.01910.97863.9844-0.34240.1415-0.21090.0715-0.0829-0.09660.1537-0.1885-0.1250.00290.0884-0.05780.39820.01570.1946-22.4955.00890.8477
79.79794.11920.47837.14024.66844.5277-0.07580.1681-0.7410.22060.1177-0.11970.5476-0.0833-0.18180.17260.01980.04130.235-0.10610.2549-8.64833.3378-13.9842
82.811-2.0583-0.12772.08121.34333.67310.2320.5749-0.5785-0.6414-0.27190.96320.7926-0.7833-0.0260.4575-0.0772-0.06480.5461-0.14610.4127-16.46620.9132-27.1559
91.65831.2157-2.3696.0851-4.01827.26640.1038-0.2792-0.09480.3656-0.3813-0.34310.19460.6660.28160.3177-0.05530.10350.72690.04940.1521-4.6091-1.5638-24.6
102.0689-0.11671.51836.35234.36446.9096-0.05510.6338-1.0365-0.27970.16630.14031.23960.5068-0.13180.6879-0.06340.11220.484-0.23080.5063-8.91-10.9868-21.7002
112.2492-0.110.43530.26240.39892.1880.1386-0.04860.16620.12180.1481-0.16710.37930.1267-0.11530.02280.1054-0.00710.31430.08920.1113-13.13555.4653-6.2218
127.3573-0.27830.85812.1504-0.22681.1480.0430.13970.0235-0.0820.07790.36990.0342-0.12060.16060.04360.1576-0.02870.77180.01820.3045-28.423510.6684-5.8479
135.14471.8914-0.95011.1155-1.85965.6120.1606-0.3390.5450.5364-0.42390.0496-0.62190.02710.05890.2672-0.0805-0.08960.09370.01090.1932-5.43873.201413.744
143.7191.48461.53011.03061.70033.9913-0.0425-0.1694-0.81050.3841-0.0512-0.51551.6112-0.1607-0.06920.7123-0.1315-0.02640.340.05680.3282-2.3617-9.067314.7679
153.0327-1.0521-0.87571.6082-0.85111.3336-0.2370.3538-0.5082-0.01560.00160.45480.587-0.6301-0.04960.541-0.2753-0.01210.39640.09440.2631-14.1382-5.57739.8434
162.9502-0.23170.6251.23760.26381.53240.18410.05410.3399-0.00190.0721-0.18590.10650.01030.065-0.17080.1004-0.10840.0840.05090.24337.288310.38797.2536
176.19467.58650.0631.9996-2.73836.74680.1245-0.0964-1.15450.62470.5676-3.41841.70473.4581-0.58860.58120.165-0.26911.0825-0.16980.8135.44841.262124.0178
187.8745.585-3.3659.1884-4.23372.1083-0.14380.53340.313-0.273-0.1160.0391-0.2153-0.0810.28480.34060.0322-0.05880.2073-0.04160.16732.07613.002622.6111
190.76871.08040.68882.0355-0.15333.0770.0774-0.04120.69290.2631-0.1169-0.0168-0.95980.27520.16870.2693-0.029-0.09220.3252-0.26420.42260.825322.220322.3161
202.58431.806-0.38836.65336.3348.9379-0.1104-0.49870.07320.43140.04970.20090.1805-0.46190.1070.4257-0.22250.05620.5363-0.16360.2801-2.423316.067430.5676
212.4559-1.2346-0.13517.08737.39238.33240.5273-0.84250.22440.55260.5824-1.3177-0.51340.9347-1.03010.6681-0.1968-0.13540.9265-0.25270.582410.569714.968232.8224
221.76870.1931-0.47461.7093-0.53490.27120.2167-0.56140.5070.7565-0.0256-0.20610.05130.39790.25080.22450.1274-0.24390.3478-0.09730.21188.622711.486620.399
234.74270.2497-0.78794.84442.09342.8626-0.1336-0.04530.9784-0.14120.3718-0.34-0.23530.3183-0.06210.07190.0862-0.02880.39160.10860.3627.299414.67761.208
241.23781.6060.28452.16560.32510.08950.26450.0718-1.20110.1571-0.1284-0.06760.85-0.409-0.42911.7153-0.4742-0.09560.7614-0.46841.6707-14.9656-30.12512.966
250.7196-0.02250.41950.98831.17031.73360.28-0.84130.06140.5957-0.50410.16160.0249-0.68030.30971.0793-0.34020.14150.7909-0.31740.4683-10.737310.333632.936
262.1374-0.04960.94281.8591-1.11151.0549-0.0078-0.30110.3070.36280.0560.0154-0.3978-0.04420.27811.4578-0.1438-0.12910.8277-0.61840.9494-5.152439.052739.483
273.78533.37851.53354.06961.44822.46120.5208-0.7424-0.17961.0761-0.4688-0.13550.4939-1.0292-0.05331.0661-0.23380.02720.9365-0.25040.4951-9.759315.23937.7228
281.3478-0.2620.1180.0533-0.02510.01050.04-0.2773-0.97780.2753-0.0540.03610.8939-0.7683-0.03751.3964-0.4844-0.04180.5710.09570.5999-16.9839-14.212822.5401
290.13340.58370.1172.75470.30670.3076-0.1696-0.12230.16020.7118-0.1947-0.3959-0.009-0.08890.13781.3688-0.55770.1330.6913-0.2371.2055-13.2805-27.52394.7928
303.0498-0.92610.32850.8774-0.53873.99160.05780.5274-0.3753-0.8022-0.0426-0.06190.23180.2112-0.84341.0103-0.03870.05980.5743-0.54910.5934-8.4364-10.3178-39.3915
313.2851.31580.55514.0914-0.03290.1150.06510.21990.2164-0.8660.3008-1.1224-1.18040.5307-0.28530.8-0.09910.0450.2966-0.00210.60335.587226.0677-17.8274
324.06564.81994.62317.18655.26595.28630.3829-0.2570.44570.64850.0558-1.384-0.95590.9901-0.39941.0686-0.2087-0.10940.4338-0.16641.09410.597439.3901-0.1794
337.22682.7786-2.73446.9598-6.37247.08750.23940.51830.7936-0.5698-0.2156-0.0565-0.0110.0945-0.0340.64620.005-0.00690.22050.14270.48492.696432.1902-14.5398
341.3882-0.09721.34821.96161.58672.7769-0.29010.6208-0.5343-1.6031-0.085-0.8155-0.22420.20240.01820.9493-0.02840.14390.5199-0.17180.4995-1.69180.3447-33.9595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 16 )A7 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 28 )A17 - 28
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 49 )A29 - 49
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 68 )A50 - 68
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 102 )A69 - 102
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 121 )A103 - 121
7X-RAY DIFFRACTION7chain 'B' and (resid 7 through 28 )B7 - 28
8X-RAY DIFFRACTION8chain 'B' and (resid 29 through 49 )B29 - 49
9X-RAY DIFFRACTION9chain 'B' and (resid 50 through 62 )B50 - 62
10X-RAY DIFFRACTION10chain 'B' and (resid 63 through 81 )B63 - 81
11X-RAY DIFFRACTION11chain 'B' and (resid 82 through 99 )B82 - 99
12X-RAY DIFFRACTION12chain 'B' and (resid 100 through 120 )B100 - 120
13X-RAY DIFFRACTION13chain 'C' and (resid 12 through 28 )C12 - 28
14X-RAY DIFFRACTION14chain 'C' and (resid 29 through 49 )C29 - 49
15X-RAY DIFFRACTION15chain 'C' and (resid 50 through 81 )C50 - 81
16X-RAY DIFFRACTION16chain 'C' and (resid 82 through 121 )C82 - 121
17X-RAY DIFFRACTION17chain 'D' and (resid 8 through 16 )D8 - 16
18X-RAY DIFFRACTION18chain 'D' and (resid 17 through 26 )D17 - 26
19X-RAY DIFFRACTION19chain 'D' and (resid 27 through 44 )D27 - 44
20X-RAY DIFFRACTION20chain 'D' and (resid 45 through 62 )D45 - 62
21X-RAY DIFFRACTION21chain 'D' and (resid 63 through 70 )D63 - 70
22X-RAY DIFFRACTION22chain 'D' and (resid 71 through 102 )D71 - 102
23X-RAY DIFFRACTION23chain 'D' and (resid 103 through 121 )D103 - 121
24X-RAY DIFFRACTION24chain 'E' and (resid 1 through 5 )E1 - 5
25X-RAY DIFFRACTION25chain 'E' and (resid 6 through 28 )E6 - 28
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 5 )F1 - 5
27X-RAY DIFFRACTION27chain 'F' and (resid 6 through 15 )F6 - 15
28X-RAY DIFFRACTION28chain 'F' and (resid 16 through 25 )F16 - 25
29X-RAY DIFFRACTION29chain 'F' and (resid 26 through 28 )F26 - 28
30X-RAY DIFFRACTION30chain 'G' and (resid 1 through 10 )G1 - 10
31X-RAY DIFFRACTION31chain 'G' and (resid 11 through 28 )G11 - 28
32X-RAY DIFFRACTION32chain 'H' and (resid 1 through 5 )H1 - 5
33X-RAY DIFFRACTION33chain 'H' and (resid 6 through 10 )H6 - 10
34X-RAY DIFFRACTION34chain 'H' and (resid 11 through 28 )H11 - 28

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